A substrate processing system is provided with a first processing unit that continuously carries out first processing on substrates transported at a velocity (V1) and a second processing unit that transports the substrates processed by the first processing unit at a velocity (V2) and continuously carries out second processing on the substrates. When the speed relationship can be set at V1 > V2 by the performance of the first processing unit and the performance of the second processing unit, a cutting mechanism and selection input mechanism are further provided in addition to a plurality of second processing units being provided. When the speed relationship can be set at V1 < V2 by the performance of the first processing unit and the performance of the second processing unit, a joining mechanism that sequentially joins a plurality of substrates that have been processed by the first processing by the plurality of first processing units and inputs to the second processing unit is further provided in addition to a plurality of first processing units being provided.