A substrate processing apparatus includes a holder configured to hold a combined substrate in which a first substrate and a second substrate are bonded to each other; a first detector configured to detect an outer end portion of the first substrate; a second detector configured to detect a boundary between a bonding region where the first substrate and the second substrate are bonded and a non-bonding region located at an outside of the bonding region; a periphery removing device configured to remove a peripheral portion of the first substrate as a removing target from the combined substrate held by the holder.