A substrate processing system (100) includes a first automated substrate transfer line or main transfer line (20) configured to transfer wafers (W) over the entire system and to transfer wafers to and from respective process sections, and a second automated substrate transfer line or auxiliary transfer line (30) configured to transfer wafers (W) inside a photolithography process section (1a). The auxiliary transfer line (30) is disposed as a transfer mechanism independent of the main transfer line (20). An OHT (31) is configured to travel around on the auxiliary transfer line (30) having a loop shape, so as to transfer wafers (W) to and from and among the respective process apparatuses in the photolithography process section (1a).