A substrate processing system includes a substrate processing module, an atmospheric substrate transfer module, a first and a second vacuum substrate transfer module, a load lock module, and a vacuum substrate transfer robot. The first vacuum substrate transfer module having a first transfer space is disposed adjacent to the atmospheric substrate transfer module and the substrate processing module. The second vacuum substrate transfer module, having a second transfer space in communication with the first transfer space and external dimensions smaller than those of the first vacuum substrate transfer module in a plan view, is disposed on or under the first vacuum substrate transfer module. The load lock module is disposed between the atmospheric substrate transfer module and the second vacuum substrate transfer module. The vacuum substrate transfer robot is disposed in the first transfer space or the second transfer space to transfer a substrate.