Coupled vibration of ship shafting has been a hot research topic in recent decades, but the mechanism of coupling vibration has not been fully studied. In this paper, a continuous elastic system model of a propeller-shafting test bench is presented firstly, in which the shaft is simulated by a Timensiko beam and the propeller is simulated by an elastic disc. The coupled vibration governing equations of the continuous elastic system are derived by using the energy method, and the natural frequencies of the coupled vibration are calculated and compared with the experimental results. On this basis, the hull deformation is transformed into the base displacement, and the influence of hull deformation on the coupling vibration of the propeller shaft system is discussed.