In this study, the coupled torsional-transverse vibration of a propeller shaft system owing to the misalignment caused by the shaft rotation was investigated. The proposed numerical model is based on the modified version of the Jeffcott rotor model. The equation of motion describing the harmonic vibrations of the system was obtained using the Euler-Lagrange equations for the associated energy functional. Experiments considering different rotation speeds and axial loads acting on the propulsion shaft system were performed to verify the numerical model. The effects of system parameters such as shaft length and diameter, stiffness and damping coefficients, and cross-section eccentricity were also studied. The cross-section eccentricity increased the displacement response, yet coupled vibrations were not initially observed. With the increase in the eccentricity, the interaction between two vibration modes became apparent, and the agreement between numerical predictions and experimental measurements improved. Given the results, the modified version of the Jeffcott rotor model can represent the coupled torsional-transverse vibration of propulsion shaft systems.