Vibration aroused by road roughness has a negative impact on components of fuel cell vehicle (FCV). Researches on simulation of vibrational environments in various operation conditions are conducted extensively. Electrodynamic shakers are widely used in road vibration simulation of vehicle components due to their superiorities in fast response, wide excitation band and large exciting force. A 10T electrodynamic shaking system is selected to reproduce the vertical vibration of fuel cell engine (FCE) in various conditions, and an IMC-PID controller is designed to control the electrodynamic shaker. To emulate the FCE’s vertical vibration, a tire-engine model is established in this paper firstly. Considering the stiffness and damping of suspension, engine mount and tire, it enables to describe the vertical transmission characteristic from the tire to FCE. Road roughness, vehicle velocity and acceleration are also considered as the input of this model. The FCE’s vertical vibrations are simulated and gained separately in constant speed condition, accelerating condition and shock condition. Secondly, an electro-mechanical coupling model of the electrodynamic shaker is established, which consists of two part, electric part and mechanical part. With moving coil, table and device under test (DUT) to be considered in the mechanical part, suspension mode and coil mode are reflected in this model accurately. Then an IMC-PID controller is designed and applied to the shaker’s model. These two models are simulated synchronously to verify the effect of the IMC-PID controller. The results show that this method enables the PID parameters to be tunned quickly and electrodynamic shaker to reproduce the vibration accurately.