A substrate processing system has a first processing device which processes a substrate with a first process in a first gas atmosphere within a process chamber and a transfer device that transfers a substrate in a second gas atmosphere within a clean booth, the transfer device transferring a substrate which has been processed with a second process by a second processing device or a substrate which is to be processed by that second processing device. A load-lock chamber has a substrate transfer path between the first processing device and the transfer device and there is a gas supply device which supplies the first gas from the process chamber to the load-lock chamber when the substrate is transferred between the load-lock chamber and a first processing device, and supplies the second gas from the clean booth to the load-lock chamber when the substrate is transferred between the load-lock chamber and the transfer device.