To provide a substrate processing apparatus and a substrate processing method that can accurately correct the positional shift of a substrate, in a short time, even if the substrate is large.

The substrate processing apparatus align the direction of a line connecting a first marker and a second marker of a first substrate mounted on a mounting surface of a substrate mounting base 1 with the moving direction of a gantry crane 2, based on the positions of the first marker and second marker, stores a storage unit with the positions of the first marker and a third marker, in a state where the direction of the line connecting the first marker and second marker is aligned with the moving direction, and aligns the direction of the line connecting a first marker and a third marker on a second substrate with the direction of a line connecting the first marker on the first substrate and the third marker on the second substrate computed, based on the information stored in the storage unit, while the second substrate is mounted on the mounting surface of the substrate mounting base 1.