A control device includes a storage unit that stores therein first position information indicating relative positions between one reference processing unit selected from a plurality of processing units and the other non-reference processing units; a first calculation unit that drives the transfer device while a jig formed in the shape of a substrate is held on the transfer device, and calculates a first compensation value for compensating a position deviation between a transfer position of the jig on the transfer device with respect to the reference processing unit and a first transfer target position; and a second calculation unit that calculates a second compensation value for compensating a position deviation between a transfer position of the jig on the transfer device with respect to the non-reference processing unit and a second transfer target position based on the first compensation value and the first position information.