Embodiments of the invention provide a relay protection configuration method and a relay protection system. In the relay protection configuration method, through configuring main protection and backup protection of each protected object to different CPU board cards, relay protection configuration flexibility is increased, and simultaneously because the main protection and the backup protection of each protected object is configured to the different CPU board cards, even if anyone CPU board card has a fault, the corresponding protected object only losses one of the main protection and the backup protection and does not loss all the protection. The main protection and the backup protection of each protected object are mutually independent and are spare to each other, a possibility of protective action resistance is greatly reduced and then reliability of a protection apparatus is increased.