They follow a simplified version of USCF rules. Basically, the only look at the material the side with time has. If they have only a bishop, knight or two knights, it is a draw. There are some edge cases where Chess.com's implementation doest follow USCF rules either; i.e. some of the material depends on what material the side with no time has too, such as a pawn in the case of two knights, and the site doesn't look at that at all.
Do live games on chess.com follow the FIDE rules?
BMK