In a substrate processing apparatus 1 which performs a process on a substrate W, each of multiple processing modules 2 includes at least a first processing member 21 and a second processing member 22, and substrate transfer devices 15 and 17 transfer substrates W into the multiple processing modules 2. Further, a controller 3 configured to control the substrate processing apparatus 1 stores member operating possibility information on whether it is possible to use the first processing member 21 and the second processing member 22 provided in each of the multiple processing modules 2, and the controller 3 creates, based on the member operating possibility information and process recipe information on processes to be performed on the substrates W, a transfer schedule in which the substrate transfer devices 15 and 17 transfer the substrates W into the multiple processing modules 2 in parallel.