Electronic switch passing neutral section can eliminate the problem of train speed reduction in traditional way, and improve the train passing ability. However, the transient over-voltage generated during passing neutral section not only threatens the roof equipment, but also may damages the passing neutral section equipment. In this paper, a detailed main circuit model for a certain type of EMUs was constructed, including high-voltage system and traction converter. Aiming at the specific scheme of electronic switch passing neutral section, the technical measures of preventing over-voltage by using parallel resistance-capacitance device were designed, and research was carried out according to different dead-time. The simulation analysis and the comparison of the measured data showed that the detailed EMUs main circuit model could more accurately describe the over-phase voltage and current transient process, and the amplitude of the transient overvoltage was directly related to the dead-time. Experiments verified the effectiveness of the proposed shunt resistance-capacitance protection device for transient overvoltage suppression.