As the electric locomotive goes through the electrical sectioning overlap structure, the feed’s trip and the roof insulation’s breakdown are caused by over-voltage, the transient process when the electric locomotive goes through the electrical sectioning is analyzed, and the equivalent higher-order circuit is established, the over-voltage on the neutral line is solved by using Runge-Kutta method. Based on the united model of locomotive-network-electrical sectioning, the over-voltage experiment when the electric locomotive goes through the electrical sectioning is done, the method of using RC filter to suppress over-voltage is put forward. The experiment results show that: the over-voltage decreases from 112.8kV to 68.10kV when the neutral line is installed RC filter, the impact of over-voltage on the substation and the roof insulation equipment is reduced, the security of the locomotive operation is improved.