A substrate processing apparatus and an information storage server are connected with each other through a network. A storage part of the substrate processing apparatus stores set information and a control program, for controlling operation of the substrate processing apparatus according to the set information and the control program. The substrate processing apparatus is provided with a schedule function, for transmitting a backup instructional command according to the schedule. In response to this instructional command, the substrate processing apparatus generates a duplicate of specified information stored in the aforementioned storage part and transfers the duplicate information to the information storage server through the network. The information storage server stores the received duplicate information in a hard disk as backup data. The information storage server can also store only differential data of the duplicate information. Thus, information for controlling the operation of the substrate processing apparatus can be efficiently backed up without burdening the user.