To meet the special requirements of traction transformer backup protection, a distance protection based on phase-to-phase voltage and phase current is introduced for Scott transformer. Based on mathematical model, the voltage and current transformation relations between the high and low voltage side of Scott transformer are discussed, as well as its equivalent leakage impedances. The theoretical analysis shows that the transformation of three-phase to two-phase makes phase-to-ground and phase-to-phase impedances cannot directly reflect the fault at low voltage side. There is no neutral point grounded and then no phase voltages available at high voltage side of Scott transformer, so a distance protection by using phase-to-phase voltage and phase current is introduced. The simulation results show that the distance protection can identify the fault impedances from load impedances, so it can correctly operate when faults occur.