High-speed EMUs (electric multiple-units) frequently pass through the phase-separation zone during operation. Overvoltage generated during the operation of the vehicle-mounted circuit breaker has a long duration and high waveform steepness, which accelerates the service life of the vehicle-mounted equipment and is likely to cause insulation failures. For the above-mentioned problems, the operating overvoltage characteristics of high-speed EMU were obtained by traction substation-catenary-EMUs system (SCES) analysis and experiments, thus deriving the influences of the closed phase angle and the residual magnetism of the vehicle-mounted transformer on operating overvoltage. The results showed that the voltage phase of the catenary significantly affected the operating overvoltage, and the closed switching overvoltage was small at 0–40°, 140–210° and 320–350°. The voltage on the primary side of the vehicle-mounted transformer was 60.78 kV, with the transient impact of high-frequency oscillation overvoltage of 22.71 kV, and an initial period of oscillation of 0.01 ms. Then, the period became longer, and it took 0.5 ms for the high-frequency oscillation from attenuation to disappearance. Finally, a scheme of series reactance suppression devices was proposed to protect vehicle-mounted voltage transformers. This work is to provide data support for the insulation design and system protection of a traction power supply system.