Charlie Kaufman, neat and tidy and with his shirt tucked in, is talking about the Oscars, where he was nominated for his latest film, Anomalisa. "It was a thoroughly miserable occasion," he wails. "There's all the neuroses, the anxiety and competitiveness, all in one room. I hated it." You wouldn't want Charlie Kaufman any other way.

He is Hollywood's most unconventional screenwriter. He's already got an Oscar, for his screenplay (they need to invent a new category for the stuff he does) of Eternal Sunshine of the Spotless Mind, as well as three other nominations, so you'd have thought he might be used to it by now. And, anyway, I venture, for a film as depressed as Anomalisa, nominated in the animation category, winning an award might have seemed, well, counter-intuitive.

"No, it would have suited us to win, believe me", he retorts about his remarkably realistic stop-motion animation, which follows a miserable motivational speaker in a soulless Cincinnati hotel. "There's nothing pleasant about losing, especially after we'd been through a long process of continued losing throughout the awards season. But it makes it worse when you've created something like Anomalisa and then Woody the Cowboy and Buzz Lightyear are on stage introducing your category at the Oscars."

He shakes his head ruefully.

Anomalisa is certainly not a children's movie. It features nudity, raw emotions, swearing, drinking, smoking and full-on yet rather tender puppet sex. David Thewlis (whom Kaufman had wanted to work with since he saw the British actor in Mike Leigh's Naked) voices the 12-inch-high puppet of Michael Rose, who is staying the night in Cincinnati as keynote speaker at a business conference in the faceless, corporate Hotel Fregoli.

Michael, a married man with a family back in Los Angeles, is seized with loneliness, regret and depression. He gets drunk and calls up an ex-lover, only for their reunion in the hotel bar to go horribly wrong. He soon strikes up a relationship with another woman called Lisa (voiced by Jennifer Jason Leigh) and the pair have drunken sex in his hotel room, with all the attendant recriminations the next morning.

It isn't your usual animation and indeed started out as a "play for voices". It only began to take its current shape when Kaufman met Duke Johnson, a young animator, and the pair co-directed the project.

"We worked on the faces and the characters' look together," recalls Johnson, sitting next to Charlie on the big hotel sofa. "We did everything together in terms of the direction and the animation because we knew how these characters looked would determine the aesthetic of the film, and the emotional range of the world."

They created a highly naturalistic look for the city and the hotel, with amazing details for things like taxi meters, showers, clouds, cigarette packs and cocktail glasses. However, the puppet faces are strangely alienating, with blank stares and visible cut-out sections which makes it look like they're all wearing clear, wire framed spectacles. Aiding the alienation effect, is the fact that aside from Michael and Lisa, every other character, from the waitress to the taxi driver to the hotel manager, speaks with the same voice, that of actor Tom Noonan. In the credits, he's simply billed as: Everyone Else.

Thus Anomalisa builds on its absurdity and mundanity to create something ineffably moving and profound, not that you can quite put your finger on what that mood is, or what it all might mean.

"I do know the feeling you're talking about," says Kaufman. "I guess it's there in the writing but it was also there in the voice recordings we did. Although the actors knew it was going to be an animation, they had no idea what it was going to look like. I think they were surprised when they saw the results. Then again, so were we."

Anomalisa is, it should be mentioned, very funny. There aren't jokes as much as quirks, surreal details and arch observations on the dimness and the dullness of everyday life and the banality of conversation. One of the funniest moments has Jennifer Jason Leigh's Lisa sing Cyndi Lauper's Girls Just Want To Have Fun - but it also grows into one of the most moving scenes I've seen in the cinema this year.

Kaufman's screen universes are very concerned with the inner workings of his head, or at least of someone's head. Adaptation featured a battle between a character named Charlie Kaufman and his fictional brother Donald, both concretised in the film by Nicolas Cage; Being John Malkovich was about a puppeteer who finds a portal into John Malkovich's head; and Charlie's stab at directing his own work became Synecdoche, New York, a brilliantly baffling film about a theatre director trying to recreate real life and reflect his own soul on the world's largest theatre set.

With his interest in the workings of the mind, I wonder if the title Anomalisa came from any clinical condition, much like one of Kaufman's heroes Woody Allen who really wanted to call Annie Hall after the depressive state of Anhedonia.

"Actually, no," he says. "But the hotel Fregoli in the movie is named after a syndrome called Fregoli delusion in which people believe different people are in fact one person in different guises and forms. But 'anomalisa' was just a play on words which occurred to me in the writing, as the character happened to be called Lisa and then the word 'anomaly' came up, and it seemed a good sort of joke."

The mention of Woody Allen leads to my inevitable question of Jewishness in his work. "I don't know what you're talking about," is Kaufman's snap response and I can't tell if he's joking, at all. "I mean, you know, I am who I am," he continues, stuttering a bit, and playing with his beard. "I was raised sort of Jewish but secular, you know, I'm not from a religious family, but certainly Woody Allen was very important to me growing up, but then so was Monty Python, and I don't think any of them were Jewish?"

It's clear the Jewish question has troubled him. Naturally, I ask more about how Allen influenced him. "He was just so funny and I loved his writing when I was a kid, you know the books and his stand-up comedy - they just amazed me. I just sort of thought I want to be able to write like this… some of the stuff he wrote and said on those nightclub albums, they just stuck with me forever, like that joke about when he was taken hostage, his parents snapped into action and rented out his room. I mean it's just so perfect, I thought. But, I don't know, is it Jewish?"

He says this with such a shrug, that I laugh at how Jewish he just sounded. "Sure, the inflection is Jewish, but are those Woody Allen jokes themselves Jewish? Maybe that's the Jewish tradition, I don't know - Woody was a big admirer of Bob Hope, and you can't get less Jewish than Bob Hope, so…" He tails off.

I agree with him that he himself may not be in the Catskill tradition of Jewish comedy but, I also venture, without it I'm not sure he'd be able to exist. This clearly puzzles him. I wonder if he has tracked changes in Jewish humour and how it has changed since, say, the heydays of Woody Allen and Mel Brooks. Does the weight of his own influences sit on his shoulders as he writes?

"No, I think this is all in your head," he tells me. "I have absolutely no responsibility to any tradition or influences. When I'm writing I try to be funny, if funny is what's needed, or if I want to be honest, it's to be honest. That's it. I don't think anything about the tradition or trajectory of anything. I just think what's a cool way to tell this story, and if, you know, if it seems cool to me and those ways might come out of that tradition, but I'm not consciously trying to take that tradition forward or anything."

I object that he can hardly blame me for what's in my head as I watch his work, given that his work is so concerned with minds and heads, with split or multiple personalities and internal voices.

"Well, it's hard to know, I guess. So many things were influential to me in terms of my sense of humour. Woody Allen is certainly one of them, but National Lampoon, and Python and Lenny Bruce, who was Jewish obviously, but very different than Woody, so, and, er, Kafka. Mel Brooks, sure.

"But I think Louis CK has got a lot of surreal stuff that appeals to me and he isn't Jewish as far as I know. Well, there's Albert Brooks who's like a generation above, but great and, oh yes, I love the Coen brothers. Yes, they are Jewish, now you say it, but that's not something I think about when I'm watching their films, you know, it's not like, 'Jews are at work here'…" I daren't mention that, actually, Louis CK's grandfather was a Hungarian Jew.

I can't help feeling something very Jewish in his febrile, nervous on-screen worlds. I don't mean it as an insult or as a reductive view of his work. Indeed, I'd love to see more of Charlie Kaufman's work. "So would I," deadpans the 57-year-old.

And he looks a little sad. "No one is in such a rush to make the things I want to make," he says. "It's not about writing - I can do that pretty quickly, actually. It's just I can't get things made. After Synecdoche, which lost quite a bit of money compared to its budget, but which many people tell me is a great film, it's taken me seven years to get back to here. Well, I can't wait seven years again, and I don't have many gaps of seven years left, I'm getting older so, you know, I'd like to speed up that process but it's hard and tricky and not pleasant to go through. I get used to things looking up and then very suddenly down."

Despite losing at the Oscars, Anomalisa will surely do much to re-establish Charlie Kaufman's highly distinctive reputation? "Well, yes, in the stop-motion animation sphere, it might," he admits with another rueful grin. And he admits he may be working with Johnson again. But he's also working on a novel, as well as some repeatedly-rejected TV pilots, and there has long been talk of a Hollywood movie about a director and an internet blogger that several big names have been attached to, including Jack Black and Kate Winslet.

"I mean, it's gotten hard for everyone else, too. The studios are making very predictable movies, big movies, which I don't tend to write. I don't think I can write those. So I spend a lot of time sitting in a room, writing things no one will see."

I say I find this annoying. "I bet I find it even more annoying than you do," Kaufman replies.

And I can't come back from that. So I wish him luck and tell him I'll be telling people to go and see Anomalisa at the cinema this weekend. "I hope they listen to you," he says, and sinks back into that big sofa, like he was wishing it would swallow him up.