In traction power supply system of China High-speed Railway, the transient process of EMU has a great difference between the state of passing by Phase-separation with electric load and passing by Phase-separation without electric load. The overvoltage caused by switch in with arc in the process will influence the correct operation of the common protection device. Based on the theoretical analysis and Matlab simulation of EMU passing by Phase-separation with electric load, a feeder protection scheme applied on the EMU in the state of passing by Phase-separation with electric load based on the character of fault interphase voltage is proposed.