In Korea, five major ports have been designated as sulfur oxide emission control areas to reduce air pollutant emissions, in accordance with Article 10 of the “Special Act on Port Air Quality” and Article 32 of the “Ship Pollution Prevention Regulations”. As regulations against vesseloriginated air pollutants (such as PM, CO2, NOx, and SOx) have been strengthened, the Ministry of Oceans and Fisheries(MOF) enacted rules that newly built public ships should adopt eco-friendly propulsion systems. However, particularly in diesel–electric hybrid propulsion systems,the demand for precise control schemes continues to grow as the fuel saving rate significantly varies depending on the control strategy applied. The conventional Power Take In–Power Take Off(PTI–PTO) mode control adopts a rule-based strategy, but this strategy is applied only in the low-load range and PTI mode; thus, an additional method is required to determine the optimal fuel consumption point. The proposed control method is designed to optimize fuel consumption by applying the equivalent consumption minimization strategy(ECMS) to the PTI–PTO mode by considering the characteristics of the specific fuel oil consumption(SFOC) of the engine in a diesel–electric hybrid propulsion system. To apply this method, a specific fishing vessel model operating on the Korean coast was selected to simulate the load operation environment of the ship. In this study, a 10.2% reduction was achieved in the MATLAB/SimDrive and SimElectric simulation by comparing the fuel consumption and CO2 emissions of the ship to which the conventional rule-based strategy was applied and that to which the ECMS was applied.