Standing column well (SCW) geothermal heat exchanger permits a bleeding discharge of less than 20% in the event of a maximum load, which is an inappropriate method of using underground water. In this study, the existing operational method of two adjacent SCW geothermal heat exchangers, each with a single well, was modified. This technology aims to improve the coefficient of performance (COP) of the geothermal system by fundamentally preventing underground water discharge and maintaining a constant temperature of the underground heat exchanger. To curb the bleed water discharge, two balancing wells of cross-mixing methods were employed. The result of the cooling and heating operations with the existing SCW heat exchange system and the balancing well cross-combined heat exchange system showed that the measured COP increases by 23% and 12% during the cooling and heating operations, respectively. When operating with a balanced well cross-mixed heat exchange system, the initial temperature of the underground was constant with a small standard deviation of 0.08–0.12 °C.