There is something disarmingly and insistently humble about Chris Ware – even though he was the first graphic novelist to win a major literary prize (the Guardian's own First Book award in 2001 for Jimmy Corrigan: The Smartest Kid on Earth), even though his most recent work, Building Stories, has been acclaimed as the equivalent of James Joyce's Ulysses in form, and he has nine Eisner awards and nine Harvey awards. When I interviewed him on stage, in front of a sell-out crowd, for the Edinburgh international book festival, his first words were: "I'm not a very interesting person as you can probably already tell." We met the next day for a cup of tea, and whenever I called him a "graphic novelist", or his work "graphic novels", he replied referring to himself as a "cartoonist" and his work as "cartoons". I only learned later that "Chris Ware" is his pen name, a more unassuming version of his birth-name, Franklin Christenson Ware.

This modesty goes to the core of Ware's work, and his decision to work in cartoons. On stage he described the cartoon as a "working-class art form" and an "art of the people". He expanded on this afterwards; beginning with a short-hand history of early comics from Rodolphe Töpffer to Richard Felton Outcault, he warmed to his theme. "In America, it really exploded in the 1920s, in Chicago specifically, with the artists on the Chicago Tribune doing what were essentially serial stories that predated what would happen with radio and TV. And they were all about regular people. Take Gasoline Alley – that strip suddenly became about real life, it had a continuing narrative and a warmth. They knew the readers of the newspaper were regular people who didn't want to be talked down to. That's appealing to me: it seems like the best possible America, the point at which the ideals coalesce into a popular art form that could actually be great."

It was Of Mice and Men that first alerted the young Ware to the potential of narrative. Having been told he would flunk his English class in Nebraska after he submitted his report on Out of Africa – a picture of Africa with arrows shooting out of it – he was told to read Steinbeck and "realised a story could touch you so deeply and affect you so emotionally". That tether is the counterpart to his belief that the graphic medium stops the writer from being, as he says, "too fancy". Ware cites Charles Schulz's Peanuts as a profound influence in this regard. "Certainly as a kid I never read any comics in the newspaper with any expectation of having any kind of emotional reaction other than laughter. In America, Schulz was the first cartoonist to introduce the idea that you could empathise with a cartoon character: Charlie Brown felt bad about himself, so you end up feeling bad for him. It's Schulz in a molten core on the page. Not only do you feel for the character, you feel through the character, and that's necessary for any kind of literature to happen."

When he smiles, or pulls his mouth down in befuddlement, Ware resembles an emoticon. Photograph: Jeremy Sutton-Hibbert/Getty Images

When I ask about the influence of the Belgian cartoonist Hergé, whose illustrations are similarly geometric and precise, Ware becomes more animated. "I first discovered Tintin in an American magazine called Cricket. It was one of those magazines that kids don't like but adults do, and that adults give to children to make themselves feel better or something. I thought it was really strange because, at that point, I was reading superhero comics." (Ware had confessed on stage that he used to draw his face on to the rippling bodies of superheroes.) "I found it kind of uncomfortable; I was like, 'Is he a superhero? Is he a kid? And why is he hanging around with this bearded guy?' It was really creepy, but I liked the clarity of the drawing. I felt like I'd already seen it somehow, it had a sense of familiarity to it that I didn't really understand. I still don't, other than I think it reflects the way we reduce things when we think about the world."

Ware has a strong sense of how the mind edits continually: how two dots in a circle inevitably become a face and how simplification is one way to universalise emotions and experiences. His naivety is an aesthetic strategy, his empathy and commonality a political necessity. Building Stories gathers 14 different works about one, unnamed woman, and can be read in any order. I've read it in three of the roughly 87 billion possible permutations, and it seems like a different book each time: sometimes, the fact the character has lost a leg seems to be the motivating trauma of her life; sometimes it is her becoming a mother after having had an abortion; sometimes nothing explains her sadness. Ware says the spark for the book was a simple incident: "I saw somebody waiting for a bus, a girl who had a prosthetic leg and she was compelling as a person. It stuck with me and I ended up doing a strip about not her, but, I guess, my memory of her. I suppose we all feel like we're inadequate in some way, and there's no reason why you can't empathise with anyone, regardless of their circumstances." The book evolved into something different from Ware's initial conception. "Originally I'd envisioned the book as trying to treat democratically all the characters in the building, make them as equal as possible," he says, "but as I worked on it, it didn't feel right. I was very inspired by Krzysztof Kieślowski's Decalogue, an amazing 10-part TV drama, but it wasn't working. Then I realised everything was being filtered through the consciousness of the main character. I decided to let it go that way. I hope it's more interesting; I mean, that is the way we experience the world."

'The equivalent of James Joyce's Ulysses … Building Stories

Jimmy Corrigan had a semi-autobiographical aspect: that Jimmy only meets his father when he is an adult corresponds to Ware's own experience. Was writing the book a form of catharsis? "It wasn't emotionally taxing, but it was very emotionally interesting to me because, for better or for worse, it was what I had spent a great deal of my childhood thinking about. Probably too much. All my friends had fathers and relationships with them, and I did not. So it built up into a sort of symphonic feedback loop in my mind. I realised I had to break that, or get over it, or grow up. As I got older, I realised the emotional strength that it took my real father to finally contact me. I feel like I've failed as a son in my response to him. I was probably somewhat dismissive and unfair."

It is at this point that I secretly wonder whether Ware is human. Tall, with phenomenally long fingers and a domed forehead, he resembles a future, highly evolved form of humanity. When he smiles, or pulls his mouth down in befuddlement, he resembles an emoticon, or how a child might draw those states of mind. In his radical empathy – even extending to the father who abandoned him – he seems like all those depictions of aliens who understand what it is to be human better than humans do (indeed, future humans attempting to understand their past feature in Building Stories). That Building Stories includes work in different formats – accordion books, a version akin to a Little Golden Book, newspaper fold-outs, broadsheets – is in part a homage to and an elegy for the deadwood forms with which Ware grew up. "My great-uncle was a publisher and won the Pulitzer prize in 1919 for an essay he wrote about a race riot in Nebraska. My grandfather worked as a sports writer and editor and was eventually managing editor of the same paper. My mother worked as a reporter and editor, and then I worked briefly as a graphic designer and cartoonist, which doesn't really count, but newspapering was always around."

I ask him about newspapers in our digital age – what will happen? "I have no idea," he says. "My mum and stepfather still take a regular newspaper because they like newspapers, they like the feel, the nostalgia for having a piece of paper in front of you. I've never had that: I read my news online." And for comics? "As soon as a screen can produce something that can move, it becomes a passive medium, whereas I feel that comics are a very active medium. The appeal is they masquerade as a passive medium, but they're not at all. It takes a lot of effort to read comics, even though it seems like they're easy. It seems like they need to be fixed on paper to have a certain power – my wife always tells me never to use the word magic, but I can't help it, there is no other word: there is a magic when you read an image that you know doesn't move but you have a sense that something is moving, if not on the page then in your mind." Moving in stasis, motion leading to emotion: Ware has changed the form by his oblique humanity.

• Building Stories is published by Jonathan Cape.