In recent years, commissioning (Cx) is attracting attention as the key process for energy saving during building operation phase. This research is particularly focused on Cx in high energy-consuming building defined by the Law concerning the Rational Use of Energy. For better efficient operation, heat source system simulation is developed and considered about the combination of heating source equipments, cooling water temperature and capacity usage ratio of free cooling. The quantity control is changed when low cooling load arises in transitional season and free cooling utilization increases for the proper setting of chilled water temperature in winter. As this improvement plan is reflected the actual building operation, it can reduce the energy consumption by 219.7 MJ/m2/year, running cost by 2,289,000 yen/year and carbon-dioxide emissions by 12.4 kg-CO2/m2/year, compared to the present heat source system operation. It is also evaluated that high efficient heating source equipment, free cooling, and pump control by the inverter as energy saving techniques. The total effect can reduced the primary energy consumption by 1183.8 MJ/m2/year. It is shown that the necessary of Cx for global environment conservation in this research.