In this study, the dynamic behavior of the propulsion system of a VLCC (Very Large Crude oil Carrier) ship is investigated using a multi-input multi-output model. In this system the engine ordered speed and the number of active cylinders are assumed as inputs and the dynamic parameters of the engine such as torque and speed are considered as outputs. In this research, the effects of sea wave and wind on the system dynamic behavior have been investigated. In addition, the ship powertrain system is investigated in which the intermediate shaft and propeller shaft are analyzed using lumped parameter method, finite element method, distributed-lumped method and the results of these modeling techniques are compared to the modeling results in which the connecting shafts were considered as rigid body. Comparison of the results shows that there are significant differences between the results of rigid body method and other three types of system modeling. On the other hand, the time required to run the distributed-lumped model is much shorter compared to other methods that are considered in the study for the dynamic behavior of the ship's powertrain systems. On the other hand, the fatigue analysis of the ship power transmission shafts shows that the fatigue life assessment of these shafts is of great importance and should be considered in the design phase.