Accurate analysis and modeling of DC side short circuit transient is important for design of DC traction power supply system and assessment of the suitability of protection arrangement. In recent years, the overshoot and swing in short-circuit fault current profiles of subway traction power supply system can not be correct explained by the existing subway traction power supply system fault model. The second-order transient model on subway traction power supply system is presented by analyzing short-circuit fault current recorder, the commissioning test waveform and electrical parameters of subway train. Using this model, the simulation results are consistent with the fault recorder and the commissioning test current profiles. Also the origin of the overshoot and swing on the waveform is explained.