We conducted an operational analysis and proposed operational improvements for a large-scale hospital after updating its heat source system, using long-term monitoring data from its energy management system. Although the updated heat source system was operating appropriately, the secondary flow rate was extremely high. This posed challenges on the primary side, where many heat source machines were running to attain the secondary supply temperature. With the aim of improving the performance, we optimized the secondary flow rate to achieve a temperature difference of 5°C and modified the secondary pump control. If the operation is modified, the WTF can be expected to increase by more than three times. Additionally, this contributes to the stable operation of the heat source system. As a result, the SCOP is estimated to improve from 2.78 to 2.96 in the cooling system and from 0.92 to 0.95 in the heating system.