Provided is a substrate processing apparatus which can efficiently transfer substrates using a conveying mechanism including a plurality of substrate holding members. The substrate processing apparatus transfers a processed substrate to an intermediate conveying unit using a transport mechanism when the processed substrate returns to a substrate receiving unit. When a conveying mechanism withdraws the processed substrate from the intermediate conveying unit and transfers the processed substrate to the substrate receiving unit, a control unit determines whether both of a first substrate processed first among a plurality of substrates withdrawn from the substrate receiving unit as a set and a succeeding substrate processed later than the first substrate should be transferred together after waiting until the succeeding substrate is transferred to the intermediate conveying unit or to transfer the first substrate without waiting for the succeeding substrate, when the first substrate is transferred to the intermediate conveying unit.