Like most authors, John Knowles did draw from his own life experiences to write his most famous work, A Separate Peace. I've included a link to an excellent eNotes reference site below. I'll give you the highlights and you can do some further research and study on your own.
Knowles based his work on his time spent at Phillips Exeter Academy, a boarding school for boys in New Hampshire. He graduated in 1944, so the type of school, the location, and the dates all correlate to the setting of the novel.
While there, Knowles was a swimmer, and he hurt his foot when he fell from a tree as part of some kind of secret society ritual. All of these elements can also be found in the story. No doubt there was an undercurrent of war, as well; however, Knowles is clear about the fact that the attitude of the boys andthe atmosphere at the school during his time at Phillips Exeter was neither angry nor disillusioned--crucial elements in the novel.
It's evident Knowles applied some personal experiences to his writing, but to say the novel is autobiographical would be inaccurate.