Overvoltage problem caused by electric locomotive passing the neutral section, always result in traction substation trip or the arc eroding the contact line. In order to solve this problem, a high order circuit was established to analyze the overvoltage problem and found that the time of locomotive passing the neutral section was the conclusive factor causing overvoltage, and ferro-resonance overvoltage caused by high-voltage transformer saturation was the main reason leading to equipment insulation breakdown or protection’s mis-operation. A new method was pointed out by utilizing auto-passing neutral section device force-breaking signals, speed of locomotive and contact line’s voltage phase angle to realize the locomotive passing the neutral section without overvoltage. Electromagnetic transient simulation software PSCAD/EMTDC was used to simulate the process of passing the neutral section and the overvoltage restrain method. Simulation results indicated that the new overvoltage restrain method could efficiently control the overvoltage less than 50 kV and improve the security stability of the locomotive operation.