A substrate processing apparatus includes a process module in which a substrate is processed, a first substrate storing container, a second substrate storing container, and a transferring module that conveys the substrate between locations connected by the transferring module, wherein the process module, the first substrate storing container, and the second substrate storing container are connected by the transferring module, the method including the successive steps of, conveying an unprocessed substrate stored in the first substrate storing container to the second substrate container, conveying the unprocessed substrate stored in the second substrate storing container to the process module to process the unprocessed substrate, conveying the processed substrate processed in the process module to the first substrate storing container, and introducing inactive gas into the first substrate storing container.