Ships have long been used as a means to transport large quantities of goods. Most modern ships have propulsion systems equipped with low-speed diesel engines, steam turbines, or gas turbines. However, the demand for eco-friendly ships and smart ships is increasing owing to rising fuel oil prices. Furthermore, the regulations on ship emissions such as sulfur oxide and nitrogen oxide have led to the transition from existing mechanical propulsion systems to hybrid and electric propulsion systems. since the early 20th century, countries such as the U.S.A. and Russia have been applying electric propulsion technology to commercial vessels. Since the development of electric power technology, research has been underway to equip ships with equipment such as batteries and shaft generator motors. Various vessel propulsion systems and operation modes have been developed due to the development of such equipment and environmental regulations. In this paper, we compared and analyzed the energy efficiency of hybrid power and propulsion systems in container vessels. Power management systems compatible with existing mechanical propulsion systems are not applicable in the case of hybrid powered propulsion systems. Therefore, this paper proposed a suitable operation algorithm for a hybrid powered propulsion system. For energy comparison and numerical analysis, a ship-power model, main engine fuel characteristic model, generator fuel characteristic model, propulsion motor efficiency model, shaft generator model, and battery efficiency model were developed. The proposed integrated engineering control algorithm was applied to verify the energy efficiency through simulations. The operation data of an actual container ship was used to compare the energy efficiency for different configurations of the ship power and propulsion system. Furthermore, a comparative analysis of the energy efficiencies of the propulsion and power systems was performed via simulation