The embodiment of the invention provides a control method and system of a substation system configuration file. The control method includes the steps that after an intelligent substation is put into operation, when a working team proposes a maintenance application or reconstruction and expansion application for the intelligent substation, a work ticket is given to the working team, only the working team obtaining the work ticket is allowed to download the system configuration file of the intelligent substation from a server terminal, and before one work ticket is completed, the server terminal is forbidden to modify the system configuration file; after the working team completes maintenance or reorganization and expansion work, and transacts completeness of the working ticket, the modified system configuration file uploaded by the working team is received, and the modified system configuration file is stored to the server terminal. According to the technical scheme, controlling of the system configuration file and the engineering schedule are combined, the uniqueness of the system configuration file is guaranteed, the system configuration file used in a present-operating intelligent substation is conveniently judged, and the problem that version management of the system configuration file is disordered is solved.