Over-voltage of carbody caused by lightning will seriously interfere with the operation of communication, monitoring, control and other weak current equipment, which will result in logic chaos or misoperation of the equipment. To research the carbody over-voltage of high-speed train lightning short-circuit, the equivalent circuit model of lightning current flowing through the EMUs was established according to the actual conditions. The changeable of lightning over-voltage waveforms and amplitude was analyzed when change the grounding resistance or shunt capacitor. The results showed that: trains large grounding resistance was the root cause of the carbody over-voltage; the amplitude of body over-voltage was effectively reduced by reducing grounding system impedance or shunt capacitance; When the grounding resistor shunts capacitance, wave head of over-voltage waveform time increased, and the increased rate of waveform was reduced, which could effectively restrain the impact of the over-voltage of the EMUs.