A substrate processing system includes a transfer device provided with a shelf, a batch processing device, and a single-wafer processing device. The transfer device, the single-wafer processing device, and the batch processing device are linearly arranged in a row, in the order listed herein. The batch processing device includes a first batch transport mechanism that transports a plurality of substrates to a batch process bath, for example, all at once. The first batch transport mechanism receives the plurality of substrates converted into the vertical orientation on the transfer device side, and transports the substrates to, for example, a batch process bath directly, without using a substrate transport robot in the single-wafer processing device.