There are many electronic devices in electric vehicle (EV), making its electromagnetic compatibility (EMC) 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 EV was mainly researched, and a co-simulation method was proposed: control system and motor model were established with Matlab, and the equivalent circuit model of inverter and the cable model were established with Saber. By this way, a complete motor drive system model for conductive EMI was obtained. This modeling method can not only accurately establish the EMI sources and coupling paths, but can simulate the control strategy and operating conditions. In order to study the influence of Inverter Modulation Mode on the common mode (CM) EMI of motor drive system, firstly equivalent circuit model of inverter was established with Saber, and control system of motor drive system using space vector pulse width Modulation (SVPWM) and permanent magnet synchronous motor (PMSM) was established with Matlab. Then the CM current at the output of inverter was experimented, and the accuracy of the model was verified by comparing the simulation with the experiment. Finally, the effect of random zero-vector distribution PWM (RZPWM) and random switching frequency PWM (RSFPWM) on CM EMI was researched. 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 EV.