High-speed and high-precision rotating machinery is widely applied in industry, which promotes the rapid development of non-contact bearings represented by active magnetic bearings (AMBs). The rotor-AMBs system is usually installed on the base. Due to the base motion, it affects the dynamic characteristics of the rotor-AMBs system. In this paper, the dynamic analysis of the rotor-AMBs system with base motion is carried out. The dynamic model of the system with base motion is first derived, and the control model is then established. The influence of the inherent property of the base, the excitation mode of the base motion, and the control method for the rotor-AMBs system are analyzed with numerical simulation. In addition, the combination of feedforward control and PID control is employed to eliminate the vibration disturbance caused by the base motion and improve the suspension accuracy of the rotor. The experimental results show that the proposed hybrid control can effectively reduce the vibration of the rotor-AMBs system with base motion.