A substrate bonding apparatus and method are provided. The substrate bonding apparatus may include a board having a receiving surface opposite to a substrate fixed at one side thereof, a plurality of chucking members located between the receiving surface of the board and the substrate, and a substrate separation device to separate the substrate from the chucking members. The substrate separation device includes a pusher for pushing the substrate to separate the substrate from the chucking members, and a base plate installed at the receiving surface of the board, the base plate having an installation space to install the pusher formed therein. The pusher protrudes out of the base plate through an inlet and outlet port located at one end of the installation space to pressurize the substrate.