The invention discloses a configuration data updating method and system of an optical network unit (ONU). The method comprises the following steps of: when the ONU works normally, an Ethernet passive optical network (DPoE) system based on a wire transmission data service interface specification management platform initializes a request of a trivial file transfer protocol (TFTP) to a background management system, and acquires new configuration files of the ONU from the background management system; and the DPoE system updates the acquired new configuration file onto the ONU. By using the method disclosed by the invention, seamless updating of the configuration data of the ONU on the premise of guaranteeing normal service operation is realized.