A substrate processing system, which repeats a carrying cycle in which a substrate is carried sequentially in a carrying order indicated by module numbers assigned to the modules, respectively, from the module of a lower module number to that of a higher module number, and is capable of processing substrates at a high throughput even if some modules become unusable and, thereafter, become usable. A controller controls a carrier such that the carrier carries a substrate taken out from the module preceding a multimodule unit including a plurality of modules to the module nest in the carrying order to the module of the multimodule unit from which a substrate is carried out at time nearest to time when the substrate was carried out from the module preceding the multimodule.