The invention provides a data processing method and system of a relay protection device with a plurality of plugins. The method comprises the steps that: when a trigger signal sent by a relay protection device loading management terminal on the relay protection device is received by means of network connection, the relay protection device loading management terminal is connected with a far-end server so as to receive total data packets for updating the plugins of the relay protection device and/or send total backup data packets formed by packaged data in reserved plugins of the relay protection device. According to the above scheme, the data processing method and system of the relay protection device with the plurality of plugins are provided, the relay protection device loading management terminal used for triggering backups/updating is further provided, data in the relay protection device can be automatically backed up/updated, and compared with the prior art, the working efficiency is improved, and the fault rate is lowered.