I believe that John is the author's brother. The author writes that his most vivid memories of his brother "all fill me with poignant compunction at the thought of my own pride and hard-heartedness, and his natural humility and love".
John Paul is often left at home—that is, with Pop and Bonnemaman—while the older brother gets to accompany Father. He is rejected by his older brother and his friends. He is largely left out of Thomas's life. Certainly an autobiography of John Paul Merton would bear little resemblance to his brother's. John Paul ends the book on a sad note as well when he gives his life in the war. Throughout, John Paul associates with sadness and poignancy.