The invention belongs to the field of relay protection of power systems, and particularly relates to an inter-station pilot protection system with a remote backup function and an inter-station pilot protection method. The inter-station pilot protection system with the remote backup function comprises a protection information upload module, an inter-station information interaction module and a remote backup acceleration module which are sequentially connected, wherein the protection information upload module outputs a result on the basis of a protection line interval and extracts distance protection information and zero-sequence current protection information; the inter-station information interaction module transmits inter-station interaction information on the basis of the protection information uploaded by the information upload module; and the remote backup acceleration module starts an information identification fault according to the interaction information and local protection startup information, a fault of the whole line is subjected to quick-acting removal and the fault of a lower line is subjected to remote backup acceleration action. According to the inter-station pilot protection system and method, kinds of faults can be accurately and quickly identified and located, the fault of the whole line quickly acts and the fault of the lower line is subjected to reliable acceleration action of remote backup protection.