A three-dimensional model of propeller and shafting has been established to study the influence of the elastic effect of the marine propeller on the hydrodynamic performance and structural characteristics. Taking two materials of nickel aluminum bronze alloy and glass fiber as the representatives of “rigid propeller” and “elastic propeller”, respectively, the two-way fluid structure interaction (FSI) of the propellers of these two materials is calculated in a uniform flow field. The hydrodynamics characteristics such as the fluctuation pressure, blade pressure distribution and propulsion performance, and the structural characteristics such as the blade deformation and maximum equivalent stress are compared and analyzed. The results show that the elastic effect of the blade increases the fluctuation pressure in the flow field, resulting in more uniform pressure distribution of the blade and reduction of the thrust and torque, but the propulsion efficiency varies at different advance speeds. At the same time, the elastic effect of the blade increases the blade deformation and reduces the maximum equivalent stress. This study can provide references for the propeller performance calculation and the vibration and noise reduction design of the stern for larger ships, especially for ships with long shafting and large skew propellers and underwater vehicles.