The subways are engineering construction projects with highly centralized mechatronic, electrical, and electronic systems. The lightning brings about serious threat to subway control systems, and the safety of passengers and staff personal. Through calculating of the number of the predicted lightning strikes at the elevated stations of newly built five subways in Beijing, the significance of the subway system in megapolises and the severity of lightning accident consequence and other factors are analyzed. The results indicate that the elevated subway stations (and the elevated section) are determined as the second type of buildings for lightning protection. The analysis of the lightning strike possibility of running trains indicates that the special surge protector devices should be installed in the contact rail and walking tracks according to a certain interval, so to strengthen and improve the lightning protection of traction power supply. The advantages and disadvantages of using separating series gaps in the elevated bridge grounding are analyzed. The idea of reducing or stopping the use of the separating series gaps, rather strengthening the corrosion protection design of stray current is discussed.