The force that propels the reader through Gone Girl, Gillian Flynn's almost unpleasantly gripping psychological thriller about a marriage turned rancid, is dread. She is a virtuoso of the not-quite-right detail, the skin-crawling sense that something is very wrong, that it is under your nose, yet you can't make out what it is. In an earlier novel, the way one character eats a sardine is enough to establish him as horribly creepy. ("[He] sucked it into his mouth whole. I could picture the tiny bones snapping as he chewed.") In Gone Girl, a husband's reaction to the disappearance of his wife isn't that of a murderer, but neither is it quite what you would expect from a distressed partner. The tableau is somehow askew. Flynn's book has sold more than 2m copies worldwide, but the anecdote she tells most proudly concerns her cousin: shortly after she read it, her normally frugal husband happened to suggest that they go on a luxury holiday; her first, fleeting thought was that he might be plotting to kill her.

"That's exactly my goal: to make spouses look askance at each other," Flynn deadpans, over breakfast at a diner in Ukrainian Village, the neighbourhood of Chicago where she lives. She is 42, slight and copper-haired, and accustomed to people assuming that she must have personal experience of seriously bad things: that Gone Girl's marriage of a sociopath to an arch-manipulator must be her marriage – or that the sinister, overbearingly affectionate mother in her first book, Sharp Objects, must resemble her own.

It doesn't work that way, of course. As the new novel's success has taken her to literary festivals around the world, Flynn says "the number of mystery and horror writers I've met who are just the sanest and the nicest people … it's crazy. Maybe it's because the writing gets something out of the system? It seems like the darker the books are, the nicer the person is." She narrows her eyes. "People say it's the romance writers you've got to watch out for." Her actual mother is "a cute 5ft 2in blonde, who's a teacher and the sweetest thing in the world". She likes to stand at the back of her daughter's readings and make mock-threatening gestures at audience members who suggest that Gillian (the "g" is hard, which seems appropriate) must have endured a horrifying childhood.

For the past four years, Flynn has been on a frenetic upward trajectory. It started with a setback: in 2009, months before the release of her second book, Dark Places, she was fired from her job as a pop culture writer at Entertainment Weekly magazine in Manhattan amid budget cutbacks. Yet by the end of 2012, she had published Gone Girl, given birth to her first child, a son, and written the screenplay for the movie version of the novel, which is being produced by Reese Witherspoon, and directed – at least according to widely reported rumours – by David Fincher. (A film of Dark Places, starring Charlize Theron, is also nearing completion.) Gone Girl, the New York Times reviewer Janet Maslin enthused, attained "Patricia Highsmith's level of discreet malice". The book reached No 1 in that paper's bestseller lists last July.

A similar initial fate – being fired from a New York pop culture magazine – is what sends Nick Dunne, the husband of Gone Girl, back to a rented McMansion in his native state of Missouri, resentfully accompanied by his beautiful, perfectionist, trust-fund-supported wife, Amy. It's in Nick's crumbling Mississippi River hometown that he returns home one afternoon to find the front door swinging open, signs of a struggle in the living room, and no trace of Amy. (On the other hand, the kitchen is clean, and the cat has been fed.) The story unfolds in alternating perspectives: entries from Amy's diary, from the day she met Nick to the day she vanishes, and Nick's account of the weeks following her disappearance. Neither narrator seems entirely reliable, and something is off-kilter from the first paragraph. "When I think of my wife, I always think of her head … you could imagine her skull quite easily," Nick muses, as he comes downstairs to encounter his wife humming the theme from MASH – "suicide is painless" – to herself in the kitchen.

Little more of the story can be summarised without ruining the vertiginous (and, to me, utterly unexpected) plot twists that Flynn has in store. But it can be safely noted that her theme is the profound impossibility of ever knowing someone else's mind, even in the supposedly intimate context of a marriage. She had barely got married herself – to a lawyer, Brett Nolan – when she wrote it. Was her experience as a newlywed really so dark? "We were very newly married at the time," she says, as if slightly surprised to do the calculation herself. "But part of it is that I'm a grand worst-case scenarist in my personal life, so I was doing a lot of: 'What is marriage? What should it be? What shouldn't it be?' The funny thing, I guess, is that my husband ended up being the muse of a book about the worst marriage in the world, because if he hadn't consistently said, 'Don't censor yourself, don't worry about me' – if he'd been anxious and worried about it – then it would never have gotten written."

This is a recurring theme in Flynn's life: the psychological bungee-jump that permits an author to plunge into barbarity precisely because she's securely moored in its opposite. Flynn was born in 1971 in Kansas City, Missouri – not to be confused with Kansas City in Kansas, just across the state border – to two college teachers. Her father taught film, and had a passion for horror, so her childhood exposure to terror was both intense and fairly easy to escape, by switching off the VCR or leaving the cinema. She watched Psycho, Alien and Bonnie and Clyde at an age when one probably shouldn't. "I watched Psycho a million times," she once told an interviewer. "In the mirror, I obsessively practised the final shot of Anthony Perkins: the Norman Bates smile right at the camera. I can still do it really well." Cinematic and literary references pervade the books: Sharp Objects borrows the most unsettling elements of Rosemary's Baby and Twin Peaks; Dark Places, which centres on the slaughter of a family in a remote Kansas farmhouse, is partly a homage to In Cold Blood – though it draws heavily, too, on Flynn's own familiarity with the strangely creepy wide expanses of America's midwest.

The most persistent charge against Flynn's books concerns their sexual politics. (Be warned that some readers may interpret the following as a spoiler.) Gone Girl's plot turns partly on one female character fabricating a charge of rape – "a trope that exists because it's powerful," Eva Wiseman wrote in the Observer, but that "perpetuates an idea that rape can be complicated"; others have accused her of peddling "misogynist caricatures", and of "a deep animosity towards women". More generally, it's true of all Flynn's novels that her women can be reliably predicted to outdo the men in their capacity for moral depravity. Flynn identifies herself as a feminist, but does she worry that she's damaging that cause in the quest for narrative shocks?

"To me, that puts a very, very small window on what feminism is," she responds. "Is it really only girl power, and you-go-girl, and empower yourself, and be the best you can be? For me, it's also the ability to have women who are bad characters … the one thing that really frustrates me is this idea that women are innately good, innately nurturing. In literature, they can be dismissably bad – trampy, vampy, bitchy types – but there's still a big pushback against the idea that women can be just pragmatically evil, bad and selfish ... I don't write psycho bitches. The psycho bitch is just crazy – she has no motive, and so she's a dismissible person because of her psycho-bitchiness."

Writing on her website, she concedes that hers is "not a particularly flattering portrait of women, [but that's] fine by me. Isn't it time to acknowledge the ugly side? I've grown quite weary of the spunky heroines, brave rape victims, soul-searching fashionistas that stock so many books. I particularly mourn the lack of female villains." It should probably be added that her lurid plots make no claim to social realism: to interpret her evil female characters as somehow representative of their real-life gender, you must willfully overlook hundreds of pages of other people and events that you'd almost certainly never encounter in reality, either.

Flynn originally planned to spend her career confronting non-fictional evil: she trained in journalism at Chicago's Northwestern University with the intention of becoming a crime reporter. But during student reporting assignments, she recalls: "I found out really quickly that that wasn't going to work for me. I just don't have the necessary skills to get in there and ask the right questions and do it sensitively. The best crime reporters don't mind charging in – but they also know how to do it as decent human beings."

The protagonist of Sharp Objects is a young reporter named Camille Preaker, sent back to her hometown to investigate a series of child killings; her agonised, fumbling attempts to doorstep bereaved relatives show "exactly the kind of reporter I would have been," Flynn says. "And I'd have been going around dreading every aspect of my life, which didn't really seem like a good way to live. So I switched very quickly: 'You know what I'm good at? Television and movies!'"

Her immersion in celebrity culture wasn't wasted, though. It informs some of Gone Girl's blackest comedy: in the days after Amy's disappearance, as the media circus grows, Nick is paralysed by self-consciousness, thanks to his awareness that the husband is always the No 1 suspect. "We'd all seen these news conferences before – when other women went missing," he muses. "We were being forced to perform the scene … I had worried about my voice wavering, so I overcorrected and the words came out clipped, like I was reading a stock report." Once everyone involved, and everyone watching, knows the grooves of the media narrative, how could anyone in the cameras' glare possibly behave "naturally"? As Flynn puts it: "The assumption is that he's not mourning correctly, so he must be a sociopath – when in reality, in that intense situation, you'd almost have to be a sociopath in order to give the media the playacting they want."

It's surprising – given the way that the denouements of Flynn's novels make you feel as if the truth had been hiding in plain sight all along – that she doesn't plot them in advance, instead pursuing numerous dead-ends and "writing the equivalent of two books for every one that gets published". She describes herself as obsessive about the thriller writer's responsibility to play fair: "One of my biggest peeves is when the writer hasn't given you enough information to figure everything out. You should be able to go back to the beginning of Gone Girl, after you've already read it and you know everything, and say: 'Check – check – yes, she gave us that information.'" Though Flynn cites Agatha Christie as the crime novelist she most admires, "even she will sometimes allow a plot to be resolved just because Poirot has 'a gleam in his eye', or whatever, and you'll realise that he knew something we didn't."

Flynn does her writing in a small, semi-underground room attached to the Victorian house she shares with Nolan; it's only accessible through "a genuinely creepy unfinished basement", and the windows look directly on to a brick wall. It's not hard to see how such surroundings might engender the mood that pervades her books. "For me, suspense is always harder and better than going for the quick, outright scare," she says. "What's scary is that psychological mind-place: not the serial killer roaming around outside, but that sense of not quite being comfortable in your own skin – of being in your own home but not being quite safe, and not being entirely able to figure out why you feel that way."

In the early afternoons, she surfaces from the gloom into daylight, to play with her son for an hour or two. "Then it's back down through the basement again, to write about murder," she says, perhaps a little too brightly.