To mark the 25th anniversary of the publication of Maus, the only comic ever to win a Pulitzer prize, its creator, Art Spiegelman, brings you a big, fat book called MetaMaus. How to describe this extravaganza? In essence, it's a nerd's guide to Maus: sprawling and definitive. There are transcripts of Spiegelman's interviews with his father, Vladek, a Polish Jew who survived Auschwitz, and whose story Maus tells; a long and exhaustive interview with Art, plus shorter ones with his wife, Françoise, and his children, Nadja and Dash; early draughts of Maus artwork; and copious examples of his many and various influences, from Donald Duck to Primo Levi. Should all this still not be enough, attached to its cover is a hyperlinked DVD, containing a Maus audio archive. If you like comics, are thinking of entering Mastermind any time soon and are stuck for a subject, here is the answer to your prayers.

My favourite part of the book, though, is the section in which Spiegelman reproduces the rejection letters he received when his agent, Jonathan Silverman, first sent Maus out to publishers. Oh dear. This is embarrassing. Behold New York's literary taste-makers acting like a bunch of cowardy custards. "Thank you for letting me see Maus," says Hilary Hinzmann, of Henry Holt. "The idea behind it is brilliant, but it never, for me, quite gets on track." Gerald Howard, at Penguin, is a little more up front, but still, he won't quite take all the blame for turning it down: "In part, my passing has to do with the natural nervousness one has in publishing something so very new and possibly (to some people) off-putting. But more crucially I don't think Maus is a completely successful work, in that it seems in some way conventional."

At St Martin's Press, Bob Miller admits that he found the book "quite affecting" (hell, he even managed to read right to the end). But what on earth would he tell the sales department? "I can't see how to advance the thing into bookstores." Even the great Robert Gottlieb of Knopf, publisher of Catch-22, doesn't get it. "It is clever and funny," he writes. "But right now, we are publishing several comic strip/cartoon type books and I think it is too soon to take on another one."

In his ramshackle SoHo studio – a sort of comics library with a membership of just one, it consists of a dingy bathroom, a kitchenette, a drawing board, the odd dusty plant and about eight million quietly groaning books – Spiegelman lights yet another cigarette. (You would be more likely to see a giraffe wandering down Mercer Street than a New Yorker who smokes with quite his dedication.) He then gives himself over to crowing delightedly. "I've met a number of editors over the years," he says, eyes rolling. "And all of them claim to have discovered Maus, when all they really have the right to claim is that they rejected it. One of them [the aforementioned Hilary Hinzmann] actually said it was too much like a sitcom." Still, no hard feelings. "If I'd heard the short-form description of it, I might have put it in the out-tray, too. It's a comic book! About the Holocaust! Oh, great. And there are mice in it! [for the uninitiated, Spiegelman's Jews are mice, his Nazis are cats, his Poles are pigs and his Americans are dogs].

'You can't blame them. There was a bookstore in my neighbourhood that kept Maus on its table of new releases for years. So, finally, I introduced myself. 'This is so, fantastic,' I said. 'The way you keep my book here.' But the manager, who was really grumpy, said, 'It's only because I can never figure out where to put the damn thing!'" He sniggers. "I guess that would sit badly with a publisher. I mean… do you put it near Garfield, or what?"

The book, which was finally published by Pantheon in the US, was a New York Times bestseller, has been translated into 18 languages and has won numerous prizes. "It has become canonical," says Spiegelman (false modesty – or any other kind of modesty, in fact – is not really his thing). "There's no way out of it: if I were a blues musician, it would play in car commercials. It has entered the culture in ways that I never could have predicted." Its success, however, took him by surprise at first – and it led him towards a kind of nervous breakdown. For a while, he didn't know if he would be able to produce the second volume (Maus II eventually came out in 1991). "I didn't know how to proceed through the gates of Auschwitz," he says in MetaMaus (the first book ends as Vladek and Art's mother, Anja, are betrayed by the smuggler who is supposed to deliver them from German-occupied Poland to safety in Hungary). "I think that the shock of being celebrated, rewarded for depicting so much death, gave me the bends..."

Art Spiegelman and his wife, the New Yorker’s art editor, Françoise Mouly, at the time of Maus’s launch in 1986. Photograph: Roger Ressmeyer/Corbis

Even after Maus II was complete, it felt, sometimes, like a kind of curse. "Maus is an ongoing problem for me, and for other comic artists," he says, now. "It was a paradigm-shifting book. Afterwards, comics were no longer jejune adventures for kids – blah, blah, blah – and so every new comic book must be compared to it. Mass culture is so fucking stupid. It says that what's important about Maus is that it's about the Holocaust. Sure, Maus cut through a lot. Suddenly, you could write about really serious things in a comic. But in the caricature version, that ended up as meaning that things [always] had to be ponderous." He flicks his lighter yet again, leaning prayerfully towards its flame. "I suppose you could say that the rest of my life has been spent figuring out how to walk around it."

The shock of Maus, and the source of its great and enduring power, lies in Spiegelman's absolute refusal to sentimentalise or sanctify the Survivor, in this case, his father. During the war, Vladek lost his six-year-old son, Richieu, poisoned by the aunt to whom his parents had sent him for safe-keeping, in order that he might avoid the gas chambers; he lost most of his extended family, and he endured months of the most appalling fear and hardship in Auschwitz-Birkenau and, later, Dachau. But unimaginable suffering, Spiegelman wants us to understand, doesn't make a person better; it just makes them suffer.

For this reason, he sets the European part of Vladek's story against his later life in Queens – Vladek, Anja and Art, who was born after the war, emigrated to the US in 1951 – where Art, with whom he has a strained, fractious relationship, painstakingly interviews him, in the hope of turning his tale into his first book (Anja committed suicide in 1968). Vladek, we grasp immediately, has grown into a thoroughly exasperating old man: stubborn, parsimonious, bullying. He is guilty of casual racism (he refers to black people as "shvartsers" and expects them to steal from him). He treats his despairing second wife, Mala, another Holocaust survivor, like a servant. He considers his only surviving son, who cannot mend a roof and has failed spectacularly to become a doctor or a dentist, to be a failure.

Art, at least as he tells it in his book, can barely stand to be in the same room as him for more than five minutes – unless, of course, he is talking about the war. "This is the oddness of it," he says. "Auschwitz became for us a safe place: a place where he could talk and I would listen."

Vladek died in 1982. Does Spiegelman miss him? Just for a beat, he falls silent, the only time in our 90-minute conversation this happens (he talks even faster than he smokes). "I can't quite answer that," he says. "Not exactly. I don't believe that another 10 chances would have gotten me there [reconciled us]. On the other hand, I could be more tolerant now. I miss my mother. But my father is always a problem. Parents are these weird creatures. They don't have scale. They're about 100 feet high when you see them from down there on the rug, and no matter what you do, no matter if you have an incredibly useful shrink, as I did, they pop back up to that size thanks to some early wiring in your brain."

Did writing Maus, in which his father is depicted with cool remorselessness, feel like an act of betrayal? "Having a writer in the family is to have a traitor in it; it's basic to the project. But… looking back, I really don't remember going to ask my pop if he would play ball. I've tried, but I just can't conjure those moments. He brought me paper, it had adverts for winter coats on one side of it – this was when he was working in the rag trade – but you can hardly build a fun childhood around bits of paper with winter coats on them. I just found him… maddening."

In Maus, however, Vladek's rumbling belligerence has another function, too: it is another way of disarming those – we might call them the "never again" brigade – who would draw easy morals from the book. Spiegelman was determined that Maus be "exempt" from certain things. "It's not a book about Israel," he says, with a grin. "Because, fortunately, my parents turned right and not left when they left Poland [the couple were miraculously reunited in Sosnowiec some weeks after the war ended]. And it's not a happy ending story like Schindler's List, where all those nice old people stand around at the end. I have a friend who says those old people should really have appeared in every scene, shouting at all those handsome movie actors, 'Pastrami? You think we had pastrami?'" He loathes "those standard Holocaust tropes".

As he sketched – completing the project took him some 13 years in all – he had the odd but thrilling feeling that he was working on something that was both "enormous" and bracingly containable. "The mouse metaphor allowed me to universalise, to depict something that was too profane to depict in a more realistic way, but my father's personal trajectory was also relatively small… I mean, I read about Treblinka, where there were no survivors [see footnote]. But I could think: to hell with Treblinka, my parents weren't there!"

He knew his animal metaphors would break down in the end (how, for instance, to show that Anja, hiding in a cellar, was afraid of rats?). But this suited him just fine. A Jew, Jean-Paul Sartre said, is someone other people call a Jew. His scheme emphasised just how dumb it was of the Nazis – or anyone – to lump humanity into arbitrary groups.

The book was acclaimed, but it had its critics, too. "When I first talked about it [in public], there were just these shouting matches with the audience. I couldn't say anything about Israel, about how nation states are not a satisfactory answer; people would go berserk." Though his Jewishness was hardly a secret – "or not to anyone who could read my last name" – Maus made him overtly Jewish to the world, and this has been a complicated business because, as he puts it in MetaMaus: "The only parts of Jewishness I can embrace easily are the parts that are unembraceable. In other words, I am happy being a rootless cosmopolitan, alienated in most environments that I fall into. And I'm proud of being somebody who synthesised different kinds of culture – it is a fundamental aspect of the diaspora Jew. I'm uneasy with the notion of the Jew as a fighting machine, the two-fisted Israeli." Do his enemies accuse him of being self-hating? "Oh, sure. Usually, I just fall back on Woody Allen and insist that it's not that I'm a self-hating Jew – I just hate myself. Or, even better… a friend of mine was attacked by Alan Dershowitz [the controversial defence lawyer] for being a self-hating Jew and my friend told him, 'I don't hate myself. I just hate you!'" He sniggers.

Spiegelman, who was born in Stockholm in 1948, grew up in Rego Park, Queens, a devoted reader of Mad magazine. He attended college – the plan was to read philosophy – but did not graduate and, in 1968, suffered a brief but intense nervous breakdown, an episode he periodically refers to in his work. (It was soon after he left hospital that his mother committed suicide.) Thereafter, he worked in the underground comics scene and – this relationship lasted for 20 years – at Topps chewing gum, where he designed Wacky Packages, a series of collectible stickers. Then, in 1976, he met Françoise Mouly, a French architecture student. They married and began producing a comic showcase called RAW on the printing press she had installed in her SoHo loft. It was in RAW, with its crazily erratic publishing schedule (11 issues in about as many years), that the very first Maus stories appeared. "Our big problem when we did RAW was the business end of things," he says. "We found it difficult to get up before the banks closed." In Maus, Mouly is depicted as calm and wise. "Yeah, in the book she functions as a stabilising rod that keeps the nuclear plant from exploding, and she definitely has that role in my life. But she has her own madnesses. She's nuts."

In 1993, Tina Brown, then editor of the New Yorker, published a controversial cover by Spiegelman, one of her new contributing editors, of a Hasidic Jew kissing a black woman. Soon after, apparently inspired by what she saw at the RAW offices, she brought Mouly to the magazine as art editor, a position she still holds (Mouly, in turn, brought with her great RAW cartoonists such as Charles Burns and Chris Ware).

Spiegelman, however, resigned from the magazine soon after the 11 September attacks (he and Mouly created the New Yorker's remarkable Twin Towers cover – a black rectangle in which the towers are picked out in silhouette in a very slightly darker shade – together). "It was fun for a while [at the New Yorker], but too much of my brain was rented out, and it was frightening, having to return to quotidian covers after 9/11. You know: 'Segways are hot! Do you have a cover about Segways?' It wasn't interesting."

But he had also become obsessed with the ideas that eventually became his book In the Shadow of No Towers, strips that the New Yorker would not publish (it drew some uneasy parallels between the horror suffered by his parents and his own experiences on that day). "The uncanny thing about 11 September is that I felt like a rooted cosmopolitan for a moment. It happened 10 blocks from my house and I felt an incredible affection for New York because it seemed so vulnerable, and it had felt so eternal and inevitable and bonecrushing. I can find that feeling again, even now, but the damn thing got hijacked so quickly. It became an army recruitment poster inside two weeks. I got used." He is disappointed that the city has elected to build new "arrogant" towers on the site of those that fell.

He thinks MetaMaus, with its elegant binding, and its varied paper textures, is "better than it had any right to be – an anniversary book is usually a kind of Sears catalogue that goes in the garbage five hours later". But is it a last gasp as well as a full stop? Does he worry that we will soon lose paper? He shakes his head, boyishly. "Yes, everybody [in publishing] is panicked, and they aren't thinking clearly. Yes, books have a function that can be partially supplanted by a little device. But there are other things that can only be experienced from the limitations of paper. Some books want to be petted. The books that have a right to be books make use of their bookness. Graphic novels – who knew that term would stick! – continue to do well because they use their bookness. Comics don't want to be sizeless."

He continues to work here, "in the studio that Maus built", on paper and on screen, but also at a log cabin in Connecticut, which, to his surprise, he and Françoise like to visit. "I have absolutely no interest in flora and fauna. 'Christmas' and 'other' are the only two categories of trees in my head. Unless it's a grizzly bear, I don't give a shit what's walking by. But this, it turns out, is great, because I can walk, and I can think, and I can solve problems in a way that I can't in New York." Does this mean that he is at work on – at last – a new long work? Some in the cartoon world snipe that he is starting to look like a guy with only one great book in him. "Ha! My stock response to that question used to be: once a philosopher, twice a pervert. Look, I am so proud of Maus. But my cells have replenished themselves several times since. I think that, finally, I am at the beginning of trying to figure a new book out. Maus does [he knocks his knuckles on the table] well enough that I don't have to chase every ambulance. I've no need of advances, and so on. That should give me incredible licence." He grins, contrarian to the last. "But who am I kidding? I guess I'll always be nostalgic for the old days."

• This article was amended on 25 October 2011. Art Spiegelman miantains that there were no survivors at Treblinka but this article is an interview with one of the few who escaped.