During the energy transition, a wind-assisted ship propulsion system has the potential for increasing energy efficiency according to the ship’s EEDI (Energy Efficiency Design Index) in the short term. However, it would not only make the diesel engine run in off-design condition, but its dynamic behavior due to time-varying wind and waves is still unknown. Hence, for a selected case used in this thesis, a Flettner rotor is chosen to be further evaluated on the system’s dynamic behavior under its favorable wind angle at Beaufort scale 6 and 7. After modeling the wind-assisted ship propulsion system, it was linearized and normalized around its static operating point. This gives more insight into the system from a frequency-domain analysis via the Bode magnitude plots of engine speed, engine torque, and ship speed to the variation of true wind speed and wakefield induced by wave amplitude disturbance. In addition to the time-domain simulation for understanding the impact of the wind and wake disturbance on the system, the system response spectrum, which was proposed as an alternative approach for analyzing the system’s dynamic behavior, was derived by connecting wind and a derived wake spectrum to the Bode magnitude plots. Therefore, how the energy is conveyed from the marine environment to the system around its equilibrium can be tracked clearly. Consequently, according to the selected case with a given controller, the results show that the fluctuation of true wind speed directly influences the ship speed, which in turn makes the engine torque be more sensitive to the variation of true wind speed in low-frequency regions. Besides, the engine speed resists to the variation of true wind speed very well due to the controller’s introduction. Although the Flettner rotor generates approximately 44% of thrust at Beaufort scale 7, the true wind speed disturbance does not result in a significant engine loading disturbance compared with the fluctuation of wakefield, which significantly influences the engine speed and torque. It was found that it is related to the frequency region where the wake spectrum overlaps with the system sensitivity function. Within this region, the controller has a relatively poor performance, and thus an engine operating cloud can be noticed in time-domain simulation. However, the ship speed is not influenced significantly by the wakefield disturbance because the frequency region of wake spectrum does not overlap with that of the transfer function where the ship speed is more sensitive to the variation of wakefield. Finally, the sensitivity study implies that a further increase of ship total mass and moment of inertia enlarge the engine speed and torque in the frequency region where the controller does not perform well. In conclusion, based on the selected case under its favorable wind condition, the potential of the wind-assisted ship propulsion system is still promising. Furthermore, the linearised model is a useful additional tool, and the system response spectrum gives more insight into the system.