GHEs are underground pipes that transmit heat between the earth and pipes. ANSYS Fluent was used to numerically investigate the thermal and hydraulic performance of a vertical twin tube ground-linked heat exchanger in a pile foundation in cooling mode. The CFD analysis uses three borehole length models—M1-10 m, M2-15 m, and M3-20 m—with flow rates from 1-100 lit/min and Reynolds numbers from 162 to 1625. The numerical results show that the average heat transfer rate of the Model M1 was 13% higher than that of the Model M2, 32% higher than that of the Model M3, and 95% higher than that of the Model M2. The pressure drop was minimal for 1 to 5 lit/min (laminar flow condition) but very high for 10 to 100 lit/min. The bore cavity length increased the pressure drop and decreased the average output temperature. These two-tube vertical GHEs with optimized length and selection of pipe materials can improve natural convection heat transfer by contacting ground waters.