Lightning failure rate is an important indicator for substation construction. Current calculation methods of insulation failure rate depend on the operation data of the substation and computer simulation, and are complex and have big errors. Thus, the rationality of substation design and the reliability of lightning protection could not be predicted. Based on the statistical method, a new method is proposed. By using the parameters of the transmission lines and towers, the lightning frequency of tower is calculated, then the lightning failure rate of substation is calculated by using the probability of the amplitude of lightning current. Taking a 500 kV HGIS substation in Guangdong Province as the research object, a simulation model is established based on EMTP-ATP, and the process of lightning striking the top of the tower and invading the substation along transmission line is simulated to determine the critical lightning current amplitude. According to the historical data of the area, the probability of the amplitude of the lightning current is obtained by fitting the measured values, then the lightning failure rate of the substation is calculated.