The rotor vibrations can be induced by the base motion in the active magnetic bearing systems. To solve this problem， a feedforward control approach based on inertial motion compensation was devised and implemented. First， a comprehensive five degrees of freedom dynamic model was formulated to describe the dynamics of a magnetically suspended rotor in the active magnetic bearing system with the base movement. Then， the rotor dynamics with various disturbance forces during small-amplitude complex base motions were analyzed. Subsequently， an innovative inertial feedforward method employing an adaptive algorithm was proposed. Finally， to verify the effectiveness of the proposed control method， an experiment platform was built， and then experimental investigations were carried out to compare the rotor's response to various disturbances both before and after activating the feedforward controller. The experimental results show that the implementation of the proposed feedforward control method led to an about 80% reduction of the vibration displacement of the magnetically suspended rotor when it is subjected to base motion perturbations. This marked reduction in displacement significantly enhanced the operational precision of the magnetically suspended rotor. Furthermore， the hardware implementation of the feedforward control method only need the addition of a compact inertial micro-electromechanical measurement unit. This small hardware addition meets some requirements for engineering applications， especially where there is very small space for the mechanical structure. In conclusion， the proposed inertial motion feedforward control method demonstrates promising ability in effectively reducing the vibration displacements of the magnetically suspended rotor disturbed by the base motion， and this can improve the operational stability and precision of active magnetic bearing systems while only a very small inertial measurement unit is added.