You can always use either word. However, "it" and "he" feel different so it is important to choose the word that fits your thoughts best. "It" sounds objective, whereas "he" sounds personal. For example, suppose you are looking through old family photographs. You see a picture of a little boy and someone asks you: "Is that your brother?" The best answer would be: "Yes, IT is". "It" sounds better than "he" because you are really talking about the photograph, not the person himself. You could also say "Yes, it is him" (or even "Yes, it is he" - both are correct.)

"Yes, it is." If the question had been "Is he your brother?" or "Is that man your brother?" then you could say "Yes, he is."