In order to analyze the influence of phase difference of propeller excitation on both sides of hull in low frequency band on the hull vibration, a transverse vibration three-beam coupling model of propeller-shaft-hull coupling system of surface ship is established based on the dynamic stiffness method. The results of the dynamic stiffness method are compared with those of the finite element method, which shows that the dynamic stiffness method is of good accuracy. The vertical natural vibration characteristics of propeller-shaft-hull coupling system are analyzed. In low frequency, the system mainly reflects the vibration of hull beam, and the propulsion shafting is of little influence on the natural characteristics of hull beam. The unit vertical harmonic forces with different phase difference are applied to the left and right propeller respectively, and the power flow from each bearing position into hull beam is calculated. The results show that the power flow into hull beam decreases with the increase of double-propeller excitation phase difference. Therefore, in the transverse vibration control of propeller-shaft-ship coupling system, it is necessary to pay more attention to the working condition when the double-propeller excitation phase difference is large.