A substrate stacking apparatus that stacks first and second substrates on each other, by forming a contact region where the first substrate held by a first holding section and the second substrate held by a second holding section contact each other, at one portion of the first and second substrates, and expanding the contact region from the one portion by releasing holding of the first substrate by the first holding section, wherein an amount of deformation occurring in a plurality of directions at least in the first substrate differs when the contact region expands, and the substrate stacking apparatus includes a restricting section that restricts misalignment between the first and second substrates caused by a difference in the amount of deformation. In the substrate stacking apparatus above, the restricting section may restrict the misalignment such that an amount of the misalignment is less than or equal to a prescribed value.