A substrate bonding apparatus includes a first chamber having a first surface plate where a first substrate is placed. A second chamber is disposed opposite to the first chamber. The second chamber has a second surface plate where a second substrate is placed. The second substrate is to be bonded to the first substrate. An alignment unit is installed in at least one of the first and second chambers. The alignment unit is capable of carrying out a six-degrees-of-freedom alignment between the first and second substrates. Thus, the substrates can be maintained parallel to each other, a spacing between the substrates can be automatically adjusted, and the substrates can be aligned in the X and Y axis directions.