Smart Spring is a kind of active vibration control device based on piezoelectric material, which can effectively suppress the vibration of the shaft system in an over-critical state, and the selection of control strategy has great influence on the vibration reduction effect of the Smart Spring. In this paper, the authors investigate the control of the over-critical vibration of the transmission shaft system with Smart Spring, based on the ADAMS and MATLAB joint simulation method. Firstly, the joint simulation model of three-support shafting with Smart Spring is established, and the over-critical speed simulation analysis of the three-support shafting under the fixed control force of the Smart Spring is carried out. The simulation results show that the maximum vibration reduction rate is 71.6%. The accuracy of the joint simulation model is verified by the experiment of the three-support shafting subcritical vibration control. On this basis, a function control force vibration control strategy with time-varying control force is proposed. By analyzing the axis orbit of the shafting, the optimal fixed control force at different speeds is obtained, the control force function is determined by polynomial fitting, and the shafting critical crossing simulation under the function control force is carried out. The simulation results show that the displacement response of the shafting under the function control force is less than that under the fixed control force in the whole speed range.