The electric compound supercharging technology can effectively solve the deterioration problem of low-speed performance of turbocharged diesel engine and hence improve the steady and transient performance of engine at low speed. For a certain exhaust-turbocharged diesel engine, the electric compound supercharging model was established by using GT-Power simulation software, and the motor and bypass valve model and corresponding control model were established in Simulink software. Through the  co-simulation of GT-Power and Simulink, the coupling relationship between the bypass valve and the motor speed during the mode switch process was analyzed for the electric compound supercharging system, the influence of the timing and velocity of bypass valve opening and closing on the intake system of engine were studied, and the method of avoiding the intake pressure and flow fluctuation during the mode switch process was put forward. The results show that the intake flow and pressure fluctuation are affected least when the electric booster is introduced by quick closing the bypass valve at the moment that the mass flow of bypass valve is approximately equal to zero, as well as when the electric booster is not applied by opening the bypass valve at the moment that the inlet and out pressure of bypass valve are approximately equal.