Spiegelman, like many of his critics, worries that "[r]eality is too much for comics ... so much has to be left out or distorted", admitting that his presentation of the story may not be accurate. He takes a postmodern approach; Maus "feeds on itself", telling the story of how the story was made. It examines the choices Spiegelman made in the retelling of his father's memories, and the artistic choices he had to make—for example, when his French wife converts to Judaism, Spiegelman's character frets over whether to depict her as a frog, a mouse, or other animal.
The book portrays different races as different species of animals—the Jews as mice, Germans as cats, and ethnic Poles as pigs, among others. Spiegelman took advantage of the way Nazi propaganda films depicted Jews as vermin, though he was first struck by the metaphor after attending a presentation where Ken Jacobs showed films of minstrel shows along with early American animated films, abundant with racial caricatures.
Jewish characters try to pass themselves off as ethnic Poles by tying pig masks to their faces, with the strings showing at the back. Vladek's disguise was more convincing than Anja's—"you could see she was more Jewish", Vladek says. Spiegelman shows this Jewishness by having her tail hang out of her disguise. This literalization of the genocidal stereotypes that drove the Nazis to their Final Solution may risk reinforcing racist labels, but Spiegelman uses the idea to create anonymity for the characters. According to art historian Andrea Liss, this may paradoxically enable the reader to identify with the characters as human, preventing the reader from observing racial characteristics based on facial traits, while reminding readers that racist classification is ever present.
In making people of each ethnicity look alike, Spiegelman hoped to show the absurdity of dividing people along such lines. Spiegelman has stated that "these metaphors ... are meant to self-destruct" and "reveal the inanity of the notion itself". Professor Amy Hungerford saw no consistent system to the animal metaphor. Rather, it signified the characters' roles in the story rather than their races—the gentile Françoise is a mouse because of her identification with her husband, who identifies with the Holocaust victims. When asked what animal he would make Israeli Jews, Spiegelman suggests porcupines. When Art visits his psychiatrist, the two wear mouse masks. Spiegelman's perceptions of the animal metaphor seem to have evolved over the book's making—in the original publication of the first volume, his self-portrait showed a mouse head on a human body, but by the time the second volume arrived, his self-portrait had become that of a man wearing a mouse mask. In Maus, the characters seem to be mice and cats only in their predator/prey relationship. In every respect other than their heads and tails, they act and speak as ordinary humans. Further complicating the animal metaphor, Anja is ironically shown to be afraid of mice, while other characters appear with pet dogs and cats, and the Nazis with attack dogs.
To Marianne Hirsch, Spiegelman's life is "dominated by memories that are not his own". His work is one not of memory but of postmemory—a term she coined after encountering Maus. This describes the relation of the children of survivors with the survivors themselves. While these children have not had their parents' experiences, they grow up with their parents' memories—the memory of another's memory—until the stories become so powerful that for these children they become memories in their own right. The children's proximity creates a "deep personal connection" with the memory, though separated from it by "generational distance".
Art tried to keep his father's story chronological, because otherwise he would "never keep it straight". His mother Anja's memories are conspicuously absent from the narrative, given her suicide and Vladek's destruction of her diaries. Hirsch sees Maus in part as an attempt to reconstruct her memory. Vladek keeps her memory alive with the pictures on his desk, "like a shrine", according to Mala.
Spiegelman displays his sense of guilt in many ways. He suffers anguish over his dead brother, Richieu, who perished in the Holocaust, and whom he feels he can never live up to. The eighth chapter, made after the publication and unexpected success of the first volume, opens with a guilt-ridden Spiegelman (now in human form, with a strapped-on mouse mask) atop a pile of corpses—the corpses of the six million Jews upon whom Maus 's success was built. He is told by his psychiatrist that his father feels guilt for having survived and for outliving his first son, and that some of Art's guilt may spring from painting his father in such an unflattering way. As he had not lived in the camps himself, he finds it difficult to understand or visualize this "separate universe", and feels inadequate in portraying it.
Spiegelman parodies the Nazis' vision of racial divisions; Vladek's racism is also put on display when he becomes upset that Françoise would pick up a black hitchhiker, a "schwartser" as he says. When she berates him, a victim of antisemitism, for his attitude, he replies, "It's not even to compare, the schwartsers and the Jews!" Spiegelman gradually deconstructs the animal metaphor throughout the book, especially in the second volume, showing where the lines cannot be drawn between races of humans.
The Germans are depicted with little difference between them, but there is great variety and little stereotyping among the Poles and Jews who dominate the story. Sometimes Jews and the Jewish councils are shown complying with the occupiers; some trick other Jews into capture, while others act as police for the Nazis.
Spiegelman shows numerous instances of Poles who risked themselves to aid Jews, and also shows antisemitism as being rife among them. The kapos who run the camps are Poles, and Anja and Vladek are tricked by Polish smugglers into the hands of the Nazis. Anja and Vladek hear stories that Poles continue to drive off and even kill returning Jews after the war.
Vladek's English is broken in contrast with that of Art's more fluent therapist, Paul Pavel, who is also an immigrant and Holocaust survivor. Vladek's knowledge of the language helps him several times during the story, as when he uses it to meet Anja. He also uses it to befriend a Frenchman, and continues to correspond with him in English after the war. His recounting of the Holocaust, first to American soldiers, then to his son, is never in his mother tongue, and English becomes his daily language when he moves to America. His difficulty with his second language is revealed as Art writes his dialogue in broken English; when Vladek is imprisoned he tells Art "... every day we prayed ... I was very religious, and it wasn't else to do". Late in the book, Vladek talks of Dachau, saying, "And here ... my troubles began", though clearly his troubles had begun long before Dachau. This unidiomatic expression was used as the subtitle of the second volume.
The German word maus is cognate to the English word "mouse", and also reminiscent of the German word mauscheln, which means "to speak like a Jew" and refers to the way Jews from Eastern Europe spoke German—a word not etymologically related to maus, but distantly to Moses.