A method, system and device for protecting a Long Reach Passive Optical Network (LR-PON) system are provided. The Electrical Relay (E-R) device receives the optical signal transmitted on two fiber transmission paths by the Optical Line Terminal (OLT) or Optical Network Unit (ONU) on one side, performs optical-to-electrical (O/E) conversion, signal regeneration, and electrical-to-optical (E/O) conversion for the optical signal, and sends the signal to the ONU or the OLT on the other side through the two fiber transmission paths. Through backup of the fiber transmission path, an LR-PON system protection method is provided to improve the reliability of the LR-PON system. The method, system, and device for protecting the LR-PON system under the present invention all support and are compatible with the existing functions of all devices in the existing LR-PON system.