The vibration and acoustic characteristics of the stern structure are significant for its reliability, comfort, and stealth performance. As there are always several intermediate and stern bearings to transmit transverse vibration between the shaft and the hull, it is more complex to control transverse vibration than longitudinal vibration. In this paper, aiming at attenuating the shaft transverse vibration under the loading system, in which external force and equipment excitation are both included, an active control model is prompted. The control force generated by the electromagnetic inertial actuator is located on the bearing support, which can attenuate the vibration on the transmission route without separating the shaft structure. Firstly, the vibration characteristics of the shaft model are gained by both numerical and experimental methods. Then based on the analysis of characteristics, the active control model for the transverse vibration is built by choosing the positions of the active control force, the reference signal, and the error signal. Lastly, an adaptive feedforward control scheme based on the Fx-LMS algorithm is chosen and the active control experiment result verifies its controllability. It provides a method for building an active control model for the transverse vibration of the propulsion shaft system under complex excitations.