A substrate transfer system to reduce total processing time by transferring a substrate at a first delivery stage to a process block where processing can be carried out earliest. The substrate processing apparatus includes a first transfer device delivering a wafer with respect to a substrate carrier, and a second transfer device delivering a wafer between a plurality of process blocks and the first transfer device via a first delivery stage, to transfer the wafer with respect to the process blocks. The process block where there is no wafer or where processing of the last wafer within the relevant process block will be completed earliest is determined based on processing information of the wafers from the process blocks, and the wafer of the first delivery stage is transferred by the second transfer device to the relevant process block. This ensures smooth transfer of the wafer to the process block.