Disclosed is an EPON system remote configuration management method. According to the EPON system remote configuration management method, a processing procedure for controlling the remote configuration function of an OLT (optical line terminal) is added into an ONU (optical network unit); the remote configuration function of the OLT is configured and managed through the ONU; by means of the packet exchanging function of the OLT and the ONU, the ONU transmits control messages for controlling remote configuration of the OLT to the OLT, and the OLT receives and analyzes the control messages transmitted by the ONU and performs remote configuration on the ONU according to analysis results. The EPON system remote configuration management method conveniently and rapidly achieves remote configuration operations of the OLT through the ONU, avoids time waste due to incapability of operating the OLT, and due to the fact that configuration operation equipment is united into the ONU, avoids frequent switching among operation equipment, thereby being simple, time-saving and intelligentized in remote configuration of the ONU.