Fuel represents a significant portion of the operating costs of voyages of the vessel. Under this situation, dramatic increase in fuel price caused a problem that earnings of ship becomes decreased seriously. Pumps in a cooling system of the vessel are often operated inefficiently. The reasons will vary from process to process and application to application. Inefficiency of pumps is one of the reason for making the cost of operating the vessel increased. This paper suggests energy-effective cooling system that controls sea water pumps with inverters to reduce energy consumption in vessel by conducting simulation with LabVIEW. Results shows that electric energy consumption of pumps are significantly deceased. If this energy-effective cooling system is applied to other systems which need cooling, it could be useful in reducing electric energy wastage.