In a substrate processing system according to the present invention, module cycle periods at a plurality of process modules PM.sub.1 through PM.sub.4 connected around a transfer module TM having installed therein a vacuum pressure-side transfer robot RB.sub.1, each representing the sum of a wafer stay time including the wafer processing time and an attendant busy time during which the wafer is transferred before and after the wafer stay time, are all set to a uniform length. The vacuum pressure-side transfer robot RB.sub.1 takes out a processed wafer W.sub.i and carries a next wafer W.sub.i+1 to be processed next by executing a pick and place operation for each of the process modules PM.sub.1 through PM.sub.4 during a single access to the process module.