There are many electronic devices in EV, making electromagnetic environment of EV complex and electromagnetic compatibility (EMC) problem serious. Motor drive system is the main interference source of EV, whose electromagnetic interference (EMI) is much worse than conventional vehicle. In this paper, the motor drive system of the electric vehicle was mainly researched, and a union simulation method was proposed: control system and motor model were established with Matlab, which is good at controlling, and the equivalent circuit model of inverter as well as the cable model was established with Saber, which is good at circuit simulation. By this way, a complete motor drive system model for conducted EMI was obtained. This modeling method can not only accurately establish the electromagnetic interference sources and coupling paths, but can simulate the control strategy and operating condition. In order to study the influence of Inverter Modulation Mode on the common mode EMI of motor drive system, firstly equivalent circuit model of inverter was established with Saber, including behavioral model of IGBT, DC bus and three phase cable model based on theory of transmission lines. Control system of motor drive system using space vector pulse width Modulation (SVPWM) strategy and permanent magnet synchronous motor (PMSM) was established with Matlab. Then the CM current at the output end of inverter was experimented, and the accuracy of the model was verified by comparing the simulation results with the experimental results. Finally, the effect of random modulation on common mode interference of inverter was researched, including random zero-vector distribution PWM (RZPWM) and random switching frequency PWM (RSFPWM). Influence of operating condition on CM EMI was also studied. The research work of this paper has a certain theoretical guiding significance for the EMI prediction of the motor drive system of electric vehicle.