Substrate processing with return processing is carried out efficiently by a substrate processing apparatus that continuously processes a plurality of substrates. The apparatus is equipped with a conveyor chamber constituting a substrate convey space, a plurality of process chambers in which substrate processing is carried out, a substrate conveying device provided in the conveyor chamber having a function of conveying substrates, and a substrate convey control device that controls the process of substrate conveyance by the substrate conveying device so that in a case in which after a substrate is continuously processed by two or more process chambers, the substrate is re-conveyed from the last process chamber to any of the two or more process chambers other than the last and return processing is implemented. In the re-conveyance, the substrate is conveyed to any of the process chambers after being temporarily retracted to a place other than a process chamber.