The invention relates to relates to the technical field of electric power, and particularly relates to a remote backup power supply automatic switching method and system. The method comprises the steps that voltage loss occurs on an operation side transformer station and the fault identification module of an operation side backup power automatic switching device does not identify the protection action of the operation side transformer station for blocking operation side backup power automatic switching, and a backup side interconnection switch closing request signal is transmitted to a backup side backup power automatic switching device; the backup side backup power automatic switching device judges whether a backup side interconnection switch meets the closing condition, and a backup side interconnection switch closing allowing signal is transmitted to the operation side backup power automatic switching device if the judgment result is yes; an operation side main power supply incoming switch is tripped off by the operation side backup power automatic switching device, and a closing confirmation signal is transmitted to the backup side backup power automatic switching device; and the backup side interconnection switch is closed so that a backup side transformer station is enabled to supply power to an operation side bus. The remote backup power supply automatic switching method and system are suitable for the working conditions with interconnection wires between the transformer stations, and the functions of mutual backup between the transformer stations and remote automatic switching can be realized on the basis of an existing backup power automatic switching system so that compatibility is high and maintainability is high.