The behavior of ship engine encountering stormy waters with different sea wavelengths has been investigated. In this study, a mathematical model is developed using governing equations for various parts of the ship, that is the hull, engine, power transmission shafts from the engine to the propeller also the propeller of the ship itself were implemented in MATLAB/ Simulink software environment. The model consists of the torsional vibrations of the transmission shafts; this enables a more accurate analysis of the engine behavior which is the source of power generation in the ship's propulsion system. The simulation results showed that the wavelength of sea waves has a significant effect on the dynamic performance of the engine. In this research, the effect of different ratios of wavelength to ship length (λ/LPp ) including 0.5, 1, 1.5 and 2 in violent stormy sea conditions with a wave height of 11.5 m and wind speed of 28.5 m/s has been investigated. The results showed that with the exception of λ/LPp of 1.5, at another ratios of λ/LPp , changes in engine performance parameters such as torque, fuel and air consumption, CO2 emission and power are decreasing with increasing wavelength. Most variations in engine speed are related to λ/LPp of 2. The results showed that by reducing the wavelength, the period of oscillations is reduced. As the ratio of wavelength to ship length increases, the number of oscillating points in the engine behavior increases and the lowest number of oscillating points can be seen at λ/LPp of 1.5. This study highlights the importance of effects of sea wavelengths as one of the most important physical parameters of the sea which should not be ignored in the design phase of the ship propulsion system and engine selection.