A substrate transfer method for transferring target substrates proceeds in a substrate processing system for performing processes including a photolithography sequence on the target substrates. The system includes a first automated substrate transfer line configured to transfer the target substrates among a plurality of process sections for respectively performing processes on the target substrates, and a second automated substrate transfer line of a cyclical type dedicated to a plurality of process apparatuses of a photolithography process section, which are configured to perform a series of processes in the photolithography sequence, the second automated substrate transfer line being located relative to the first automated substrate transfer line so as for the target substrates to be transferred therebetween. The method includes, in order to proceed with the photolithography sequence, transferring the target substrates among the process apparatuses in the photolithography process section by use of the second automated substrate transfer line.