Coaxial (CBHE) and U-type borehole heat exchangers (UBHE) are two key configurations for medium-deep geothermal energy utilization, yet systematic performance comparisons remain limited. This study develops numerical models for both systems to evaluate their thermal performance. A net heat exchange intensity metric (q), incorporating heat transfer, heat pump efficiency, and pumping power, is proposed for comprehensive system assessment. Results show that both q and the optimal flow rate increase linearly with depth. For CBHE, the optimal flow rates are 15.0 m3/h (1000 m), 17.0 m3/h (1500 m), 19.0 m3/h (2000 m), 21.0 m3/h (2500 m), and 22.5 m3/h (3000 m). At 2500 m depth, CBHEs reach peak q at lower flow rates than UBHEs, but UBHEs outperform CBHEs beyond critical flow rates of 33.0 m3/h (Shenyang) and 29.0 m3/h (Xi’an) due to lower pumping penalties. Correlation analysis identifies thermal conductivity and geothermal gradient as dominant factors affecting optimal flow rate, highlighting the need for site-specific design tailored to geological conditions and exchanger type.