A substrate processing system of the present invention includes a transfer-in/out section for transferring-in/out a substrate and a processing section for performing a plurality of processing and treatments on the substrate, in which a throughput of substrate processing at a pre-stage performed from when the substrate is transferred in from the transfer-in/out section to when the substrate is transferred out to the external apparatus is set higher than a throughput of substrate processing at a post-stage performed from when the substrate is returned from the external apparatus into the processing section to when the substrate is returned into the transfer-in/out section.