A substrate receiving method in a substrate processing system includes: a processing process of transferring a plurality of unprocessed substrates accommodated in a first substrate storage container to a substrate processing chamber in sequence and performing a plasma process on the unprocessed substrates in the substrate processing chamber; a retreating process of retreating the plasma-processed substrates temporarily to a second substrate storage container by transferring the plasma-processed substrates to the second substrate storage container in sequence; a determining process of determining whether or not the last unprocessed substrate is unloaded from the first substrate storage container; and a re-accommodating process of transferring and re-accommodating the plurality of the processed substrates accommodated in the second substrate storage container into the first substrate storage container in sequence when a substrate decided as the last unprocessed substrate is unloaded in the determining process.