As with any piece of literature, there is not "a theme" for Shutter Island. Rather, several themes are interwoven through the text. One of those themes is appearance vs. reality. Is Teddy really a US Marshal, or is he a patient in the asylum who has delusions of being a marshal and solving the mystery of a missing patient? Another theme is the effects of war and trauma on a person's psyche. As a soldier in World War II, Teddy helped to liberate the concentration camp Dachau. Throughout the story, he has flashbacks to that time and has hallucinations of a girl he was unable to rescue. A third theme may be the use of mind-altering drugs on unknowing patients. Are the patients in the asylum really mentally ill, or do the drugs they are given make them that way.
Although it is difficult to follow at times, this is a fascinating story. I hope this answer helps you.