The invention discloses a method and a system for automatically testing the relay protection function of an intelligent substation. The simulation system of the entire substation is realized in the mode that a simulation host machine is used for controlling digital relay protection and testing devices, a testing environment is provided, closed-loop testing on intelligent equipment is performed, the intelligent equipment with any scale of the substation can be tested in the mode that the simulation host machine is connected with the digital relay protection and testing devices, when tested equipment is added and the existing simulation system cannot meet the testing scale, the relay protection and testing devices in cascade connection are added to meet the testing requirement for intelligent equipment with larger scale, and besides, testing for a plurality of intelligent equipment can be realized, and the application prospect is better.