A substrate processing apparatus comprises a first substrate transfer unit having a first transfer path and a second substrate transfer unit having a second transfer path. A spin coating unit and a spin developing unit are arranged along the first transfer path, and a substrate cassette is arranged along the second transfer path. A substrate transport robot of the second substrate transfer unit selectively introduces a substrate received from a substrate transport robot of the first substrate transfer unit in one of external exposure apparatuses arranged on both end portions of the second transfer path, and discharges the substrate from the exposure apparatus for transfering the same to the substrate transport robot of the first substrate transfer unit. Thereby the substrate processing apparatus can avoid or relieve reduction of operational efficiency even if its throughput is different from that of an exposure apparatus.