A substrate processing system processes a plurality of substrates in a single-substrate processing mode by a plurality of processes and provided with a plurality of modules respectively for carrying out processes. When a defect is found in a substrate, a defective processing unit that caused the defect can be easily found out. The substrate processing system and a substrate processing method to be carried out by the substrate processing system can suppress the reduction of throughput when a large number of substrates are to be processed. The substrate processing system is provided with a plurality of modules for processing a plurality of substrates (W) in a single-substrate processing mode by a plurality of processes and includes a substrate carrying means (A4) for carrying a substrate (W) from a sending module to a receiving module, and a control means (6) for controlling the substrate carrying means (A4) on the basis of one of at least two carrying modes each assigning receiving modules to sending modules. The control means (6) changes the carrying mode in effect for the other carrying mode upon the reception of a carrying mode change command while substrates are being processed and makes the substrate carrying means (A4) carry substrates in the carrying mode newly brought into effect.