Considering that about 90% of international trade is transported via sea and ship ventilation systems consume between 3.5% and 5.5% of the ship’s rated power, ship energy consumption is of particular interest and modelling and enhancing ventilation systems are vital to reducing and optimising energy consumption. Using Computational Fluid Dynamics (CFD) simulation, modelling heat transfer and airflow patterns helped us improve the ventilation system and temperature distribution, provide thermal comfort for staff and equipment, and increase energy efficiency. We discussed the radiation effect in CFD analysis; it affected wall temperatures significantly and temperature contours to some extent; it raised air temperatures by 3 K and wall temperatures by 14 K in some areas; this issue has not been considered in previous analyses. Considering seven different engine room configurations, we analysed temperature distribution, air terminal streamlines and other parameters to choose the best. We examined four energy-saving plans for the best configuration, and airflow was reduced by 13.8% and fan power by 36% based on the temperature distribution. By improving the engine room ventilation system, average engine room temperature, heat removal efficiency, combustion air temperature, and temperature distribution developed. The analysis of air terminals included assessing their streamlines, determining areas they circulated, and customising their airflow; in addition to vertical and horizontal air terminals at the top or bottom of the engine room, we also examined a separate air terminal for engine combustion air, this tool has been used very little before.