The invention discloses a GOOSE time mark test method and a system. The system comprises a GPS main clock, a digital relay protection tester, message capturing equipment and an oscilloscope. The GPS main clock is used for realizing time setting for the digital relay protection tester and a detected intelligent terminal; at a set time T1, a contact of the digital relay protection tester is closed, switching-in shift of the detected intelligent terminal is carried out, a level signal transmitted by the digital relay protection tester is received by the detected intelligent terminal and is converted into a message, the message is captured by the message capturing equipment from the detected intelligent terminal, the switching-in shift time T2 of the detected intelligent terminal recorded in the message is recorded, a second pulse signal of the GPS main clock and the level signal received by the detected intelligent terminal are monitored and recorded by the oscilloscope to acquire the shift time T1 of the second pulse signal and the switching-in shift time T3 of the detected intelligent terminal, and time different deltat=T3-T1 is generated, and deviation of a GOOSE time mark of the detected intelligent terminal is generated according to the formula: T=T2-deltat-T1.