Abstract: A substrate processing system comprises a cassette mounting section having a plurality of cassettes arranged therein, a sub-arm mechanism for transferring the substrate into and out of the cassette within the cassette mounting section, a first transfer path of the sub-arm mechanism extending along the arrangement of the cassettes in the cassette mounting section, a process section including a heat treating section for heating or cooling the substrate and a liquid treating section in which a process liquid is applied to the substrate, a main arm mechanism for transfer of the substrate from and onto the sub-arm mechanism and from and into the process section, and a second transfer path of the main arm mechanism. The heat treating section is positioned higher than the first transfer path, interposed between the cassette mounting section and the second transfer path in respect of a horizontal plane, and comprises a plurality of compartments stacked one upon the other.