The power system is the lifeline of the spacecraft. Its reliability is directly related to the success of the missions. The short-circuit fault is a serious fault which will cause system shutdown. The protection for short-circuit fault is critical for the power systems. An accurate protection method based fault location is proposed for improving the reliability and safety of the power system of spacecraft. If there is a short-circuit fault inside the power converters, the protection switch is tripped at lower threshold immediately, then the area affected by short-circuit fault is minimized. If there is a short-circuit fault in the load side or DC bus, the protection switch is tripped at higher threshold, in order to providing enough energy to clearing the fault point. The control diagram and threshold design of the proposed protection method is provided. The simulation results are provided to verify the characteristic of the strategy. Finally, a prototype of power converter of spacecraft is also built to verify the effectiveness of the protection method.