An active vibration control method is proposed to attenuate the longitudinal vibration of a time-varying propulsion shafting system excited by the propeller force. In this method, two inertial actuators are mounted symmetrically on the thrust bearing base to suppress the longitudinal vibration, and an adaptive algorithm with online auxiliary filter estimation is applied to consider the time-varying characteristics induced by the longitudinal stiffness of the thrust bearing. The dynamic model of a shaft-foundation coupled system is established to evaluate the active control method, in which the variable longitudinal stiffness of the thrust bearing is expressed explicitly. The proposed adaptive control algorithm is compared to the conventional Fx-LMS method. Numerical and experimental results have demonstrated that the active control method is able to suppress the longitudinal vibration transmission of the foundation of the coupled system with variable characteristics, and compared to the conventional Fx-LMS method, the proposed adaptive control method is effective even in the case of a considerable variation in the control channel as the shaft speed changes continuously.