Eleanor Catton's life swerved off its expected course almost exactly 12 hours before our meeting, the morning after her novel The Luminaries – a virtuoso work set amid the 1860s New Zealand gold rush – was named the winner of the 2013 Man Booker prize.

When the moment came , the TV cameras showed a face as still as a marble sculpture, pinned into immobility by shock. Then she dove into her handbag and rootled through it until she found her acceptance speech, which she delivered in a clear but tremulous voice. "The superstitious part of me didn't want to make the speech too easy to find," she explains. "At the same time I knew I'd never be able to relax if I hadn't prepared something. At times of emotional intensity I need a script."

A person who radiates immense self-possession and quiet authority, she looks fresh and bright, despite only two-and-a-half hours' sleep; she cheerily attributes that to the fact that she hasn't taken off last night's makeup. She slept through her alarm, and more or less bundled herself into a cab for a breakfast-time radio interview, raking the previous night's pins from her hair as she did so.

Twelve hours ago Catton was a promising young writer, with two mostly well-received novels under her belt (the first, The Rehearsal, revolved around the figures on the periphery of a school sexual scandal). Now, she's a phenomenon. At 28, she's the youngest ever Man Booker-winning author with the longest-ever novel. She is only the second New Zealander to win it, after Keri Hulme, who was awarded it the year she was born. She has £50,000 in her pocket, and her book, having been a modest seller, has zoomed straight to the top of the Amazon sales ranking.

The win will mean, finally, a room of her own. At the moment she and her partner, the American poet Steven Toussaint, whom she met when they were both studying at the Iowa Writers' Workshop, rent a two-bedroom apartment in Auckland. While he works towards his PhD in poetry, "He gets the study, that's the deal. So at the moment I don't have one. The idea of being able to move into a bigger place is extremely exciting."

With the prize also comes that mixed blessing, fame, and she's already bothered by the uneven treatment accorded to men and women in the public eye.

"I have observed that male writers tend to get asked what they think and women what they feel," she says. "In my experience, and that of a lot of other women writers, all of the questions coming at them from interviewers tend to be about how lucky they are to be where they are – about luck and identity and how the idea struck them. The interviews much more seldom engage with the woman as a serious thinker, a philosopher, as a person with preoccupations that are going to sustain them for their lifetime."

And then there is the question of her youth. Though generally well-received in Britain, The Luminaries, she said, was subject to a "bullying" reception from certain male reviewers of an older generation – particularly in her native New Zealand. "People whose negative reaction has been most vehement have all been men over about 45," she says.

"One of those things that you learn in school about any kind of bullying is that it's always more to do with them than it is to do with you. I don't see that my age has anything to do with what is between the covers of my book, any more than the fact that I am right-handed. It's a fact of my biography, but it's uninteresting."

It is the peculiar constellation of her age, gender and the particular nature of The Luminaries that has, she believes, provoked "a sense of irritation from some critics – that I have been so audacious to have taken up people's time by writing a long book. There's a sense in there of: 'Who do you think you are? You can't do that.' Something else related to that is to do with the omniscient third person narration of the book. There's a feeling of: 'All right, we can tolerate [this] from a man over 50, but we are not going to be spoken to like that by you.'"

The Luminaries is, at the plot level, a page-turning, suspenseful story about a series of unsolved crimes, written in the manner of a Victorian sensation novel. In January 1866, in the New Zealand gold-rush town of Hokitika, a Scot called Moody walks into a hotel smoking room to find 12 men ruminating on a series of mysterious events: the disappearance of a rich prospector, the death of a wealthy recluse, the beating to a pulp of a prostitute. All the men are connected to these events and bound to each other.

The novel has an entirely original organising principle: each chapter is preceded by an astrological chart and each character is associated with a heavenly body; the characters act in accordance with the actual movements of the cosmos as they were, starting on 27 January 1866. At the same time, the novel is organised in 12 parts, each half the length of the previous one – thus the novel itself wanes.

These principles may look tricksy or artificial when described rather than experienced but are not, says Catton, an "exoskeleton" – rather they are entirely bound up with the ideas of the book. "The paradox is," she says, "the relationship between, on the one hand, the characters being the masters of their fates, and on the other hand that being predetermined." She talks of the astrological structure as being akin to a structure a composer might work within, and mentions her interest in the book Gödel Escher Bach, which explores patterns and systems in the work of the mathematician, artist and composer.

"One of the most baffling things is when people assume that when something is structurally ornate it is less human than something that is not structurally ornate," she says. "That puzzles me – I feel as a person the most alive and human and full of wonder when I am contemplating complexities. The ability of humans to read meaning into patterns is the most defining characteristic we have."

It's the seriousness of Catton's work that strikes you when talking to her – her belief in the novel both as a "builder of empathy" and as a carrier of ideas. When I spoke to one of the Man Booker judges, critic Stuart Kelly, he said that it was her ability to "make the novel think in a way that the novel doesn't do normally" that set her apart; the way that, for example, she sets astrology and capitalism into play as competing systems of dealing with the world, but at the same time has produced "a rip-roaring read". "The prize went to the true avant-gardist," he said. "No novel has been like this before."

For Catton – the daughter of a philosopher and a librarian – the novel is a tool for thinking with, as well as feeling with. "It is in my view a much better vehicle for philosophy than syllogisms and logical constructs," she says.

"What I like about fiction most is that it resists closure and exists, if the reader is willing to engage, as a possible encounter - an encounter that is like meeting a human being."

Correction: In an earlier version of this article, Keri Hulme's surname was spelt incorrectly.