A substrate processing system includes manufacturing process equipment including a plurality of process chambers and a control server configured to control the manufacturing process equipment. When a transporting order of semiconductor substrates is transmitted from the control server to the manufacturing process equipment, the control server provides, to the manufacturing process equipment performing an Nth process cycle (where N is a natural number) in a first transporting order, a command to switch to a second transporting order from an N+1th process cycle immediately when a restriction on at least one process chamber, into which insertion of the semiconductor substrate is restricted, is lifted.