Recently, environmental regulations have been strengthened due to climate change. This change comes in a way that limits emissions from ships in the shipbuilding industry. According to these changes, the trend of ship construction is changing installing pollutant emission reduction facilities such as scrubbers or applying alternative fuels such as low sulfur oil and LNG to satisfy rule requirements. However, these changes are focused on large ships. Small ships are limited in size. So, it is hard to install large facilities such as scrubbers and LNG propulsion systems, such as fishing boats that require operating space. In addition, in order to apply the pure electric propulsion method, there is a risk of marine distress during battery discharge. Therefore, the application of the electric–diesel hybrid propulsion method for small ships is being studied as a compromised solution. Since hybrid propulsion uses various energy sources, a method that can estimate effective efficiency is required for efficient operation. Therefore, in this study, a Bond graph is used to model the various energy sources of hybrid propulsion ships in an integrated manner. Furthermore, based on energy system modeling using the Bond graph, the study aims to propose a method for finding the optimal operational scenarios and reduction ratios for the entire voyage, considering the navigation feature of each different maritime region. In particular, the reduction gear is an important component at the junction of the power transmission of the hybrid propulsion ship. It is expected to be useful in the initial design stage as it can change the efficient operation performance with minimum design change.