There is provided a substrate transfer method capable of preventing fine particles from adhering to a wafer. A substrate processing system 10 includes process modules 12 to 17 each having therein an inner space S1; a transfer module 11, having an inner space S2, connected to the process modules 12 to 17; and opening/closing gate valves 30 each partitioning the inner space S1 and the inner space S2. The transfer module 11 includes in the inner space S2 a transfer arm device 21 for holding a wafer W and for loading/unloading the wafer W into/from the process modules 12 to 17. The transfer arm device 21 holds the wafer W at a retreated position deviated from a facing position facing the gate valve 30 during an opening motion of the gate valve 30.