Since the variable-speed seawater pump and the three-way valve of a ship’s central cooling system are forms of feedback from the same output signal, these controllers may cause interference when they are not coordinated. Therefore, studying an efficient control tuning method for a central cooling water system is necessary. In this study, a central cooling water system is modeled using Matlab Simulink by utilizing an actual operation dataset, and unknown parameters are estimated for fine-tuning. The simulation model is then verified using the second operating dataset. Additionally, transfer functions are developed for the freshwater output temperature against the three-way valve openness input and the electrical power frequency input to the seawater pump motor, supposing that the two systems are independent. Then, the two PI controllers are tuned using internal model control (IMC) filters. Moreover, the modified internal model control tuning method is suggested, using the character of the central cooling system, which has a large time constant for the heat exchanger system with the seawater pump and a small time constant for the three-way valve system. This method simplifies the tuning of the two combined PI controllers, enhancing the seawater pump’s overall efficiency and the three-way valve’s operation. This study presents the proposed tuning methods based on the IMC filter and modified IMC guide, which confirmed the simple determination of the gain values of the PI controller with the efficient control of the rotational speed of the seawater pump and the three-way valve with reasonable control of the freshwater outlet temperature.