Since the controllers of the variable speed seawater pump and the 3-way valve of a ship central cooling system receive the feedback signal from the same output, the two controllers may interfere and operate inefficiently under certain conditions. Therefore, studying an efficient control tuning method for the central cooling water system is necessary. The central cooling water system was modeled in this study using MATLAB Simulink, utilizing actual operation data, and unknown parameters are estimated to fine-tune. The model is then verified using another operating data set. Additionally, transfer functions are developed for freshwater output temperature against 3-way valve openness input and seawater pump motor electric power frequency input. Then, the two PI controllers are tuned through the Internal Model Control guide, supposing the two systems are decoupled. Moreover, the modified IMC tuning method is suggested for the seawater pump system, which has larger time constants because of a heat exchanger. This method simplifies combining the two PI controller tuning, enhancing the seawater pump's overall efficiency and 3-way valve operation. This study determined that the proposed tuning methods through the IMC guide confirmed the efficiency of controlling the seawater pump speed and 3-way valve with reasonable control of freshwater outlet temperature.