An operating efficiency of heat source system for clean room is relatively low because water temperature generated by chilling unit is lower than required from the type of heat load and control method of free-cooling is not optimized. To improve the operation efficiency, we suggest a structure of heat source system which changes supply water temperature depend on a heat load and control method which use free-cooling efficiently. As a result of practical simulation, energy consumption of heat source can be reduced higher than 30% by automatic operation and by installing chillers in each type of heat load.