There is provided a substrate processing system having high maintainability by widening a gap between various processing apparatuses connected with side surfaces of transfer modules and capable of achieving sufficient productivity by avoiding deterioration in throughput. The substrate processing system for manufacturing an organic EL device by forming a multiple number of layers including, e.g., an organic layer on a substrate includes at least one transfer module configured to be evacuable and arranged along a straight transfer route. Within the transfer module, a multiple number of loading/unloading areas for loading/unloading the substrate with respect to a processing apparatus and at least one stocking area positioned between the loading/unloading areas are alternately arranged along the transfer route in series, and the processing apparatus is connected with a side surface of the transfer module at a position facing each of the loading/unloading areas.