A local deformation which is generated on bonded substrates can be reduced. A bonding apparatus includes a first holding unit configured to attract and hold a first substrate from above; a second holding unit configured to attract and hold a second substrate from below; a striker configured to bring the first substrate into contact with the second substrate by pressing a central portion of the first substrate from above; a moving unit configured to move the second holding unit between a non-facing position where the second holding unit does not face the first holding unit and a facing position where the second holding unit faces the first holding unit; and a temperature control unit disposed to face the second holding unit placed at the non-facing position and configured to locally adjust a temperature of the second substrate attracted to and held by the second holding unit.