Reliable lightning protection of 500 kV extra-high voltage substation is essential for its safe and stable operation. In this paper, combined with the design scheme of typical 500 kV substation – Fengquan substation in west Inner Mongolia power grid, the electromagnetic transient calculation program (EMTP) was used to establish the simulation calculation model of lightning intrusion wave overvoltage of 500 kV extra-high voltage substation. Considering the configuration scheme and parameters of the lightning arrester in the substation, the lightning stroke point, the impulse grounding resistance of the tower and other influence factors, the overvoltage of the electrical equipment in the 500 kV substation was calculated when lightning wave intruded by using the deterministic method. The influence of various factors on the overvoltage was analysed, and the layout scheme of the lightning arrester in the substation was checked. Combined with the altitude of the substation, the lightning impulse insulation level of the substation equipment was checked. Moreover, using the probability and statistics method, the minimum safe operation year of the equipment in the 500 kV Fengquan substation was calculated to be 1455 years, which proved that the safe operation years of the substation equipment can meet the standard requirements. The research results can provide reference for the design of extra-high voltage engineering in west Inner Mongolia power grid.