The hydroelastic analysis of the propeller-shafting system in the non-uniform wake is a key step for designing a modern propeller-shafting system. The hydroelastic responses of the propeller-shafting system in the wake of ships are predicted by applying a three-dimensional time-frequency combined panel approach in conjunction with the finite element method. A fully non-penetration boundary condition applied on the deformed blade surface is conducted. The correction of both the incoming flow velocities and the normal vectors imposed on the blade surface of the transient vibration and the equilibrium positions is considered. The added-mass and -damping matrices due to strongly coupled fluid-structure interaction are derived. By comparing the present findings to numerical solutions calculated using the commercial tool Ansys Mechanical, the accuracy of the suggested technique is verified. It is observed that the added damping is higher, and the amplitudes of bearing forces are smaller, by applying the fully non-penetration boundary condition compared with the results obtained by imposing the other two simplified non-penetration conditions. This indicates that the designers need to imply the fully non-penetration condition on the deformed surfaces to predict the hydroelastic dynamics of the propeller-shafting system, especially in the case of high skew propellers. In addition, the amplitudes of the exciting forces after considering the fluid and propeller-shaft system interaction can be larger or smaller than those ignoring the interaction. The results depend on the phase difference and the mode shape.