A substrate bonding apparatus for bonding substrates together in a vacuum at high speeds, with a high degree of accuracy includes a first chamber C1, a second chamber C2, and a third chamber C3. Two substrates to be bonded together are loaded in the first chamber C1. The two substrates are bonded together in the second chamber C2. The two substrates bonded together are unloaded in the third chamber C3. The first and third chambers are variably controlled from an atmospheric pressure state to a medium vacuum state. The second chamber is variably controlled from the medium vacuum state to a high vacuum state.