Because you did not indicate the specific Maus I or Maus II, I assume you mean The Complete Maus which compiles both books in one. (If you wanted to be specific to the first or second part, feel free to repost your question.) In short, the main theme of Maus is the Holocaust: the difficulties during, the post traumatic stress afterward, and the father/son relationship as a result.
The difficulties during the actual Holocaust are portrayed in a very different way here in comic book form. Poland is occupied by Germany, of course. However, instead of the “human” Nazis roaming around, the German military is portrayed through prowling cats. The Jewish people, of course, are mice trying to avoid their certain death. The Spiegelman mice are put into one of the Jewish ghettos and then sent directly to Auschwitz (at the end of Maus I). Why were they sent to the worst death camp of the Holocaust? Fellow countrymen at the border betrayed them when the Spiegelmans tried to flee to Hungary in 1944. As the mice worry for their lives, the truth comes out:
If they brought you here, they'll put you to work. They’re not ready to kill you YET.
Vladek and Anja Spiegelman get separated (as all husbands and wives did) as soon as they entered the camp. They endure all of the horrors there at the work camp and are blessed enough to be reunited after World War II is over.
The Holocaust is further explored as a theme even after the horrors have ceased. In a sense, what happens to Vladek and Anja Spiegelman after the Holocaust is almost as tragic as the death camp and war themselves. Even though they are reunited after the war and even though they both survive Auschwitz, Anja ends up committing suicide to end her pain. Vladek is plagued with failing health and, worse, with bitterness. Vladek becomes miserly, grumpy, and mean to his second wife, Mala. Vladek seems unable to gain much happiness in the life he worked so hard to save.
To die, it's easy. But you have to struggle for life.
In regards to the theme of father/son relationships, this is explored through the Art Spiegelman’s struggle to record his dad’s story. Art Spiegelman, of course, is one of the mice in Maus and plays himself struggling to get the truth out of his ailing and bitter father.
I know this is insane, but I somehow wish I had been in Auschwitz with my parents so I could really know what they lived through! I guess it's some kind of guilt about having had an easier life than they did.
Even though Art Spiegelman did not live through the Holocaust, he is just as troubled as his parents. Due to his second-hand experience, Art feels complete desperation in not being able to portray the darkest reality of the death and tragedy within the death camps of the Nazis. The Holocaust, then, continues to damage people (and mice) psychologically even long after its extinction.
In conclusion, it is really interesting that this graphic theme of the Holocaust is presented in comic book form. Generally, the death and misery associated with such mass-killing would not be a good theme for a comic, but in this case Art Spiegelman is able to give the characters allegorical qualities. The Germans represented by prowling cats hungry for the Jews as scurrying mice is a fitting analogy.