In long-term operations, seasonal imbalance in the thermal load may adversely affect the heat transfer performance of the energy piles, potentially resulting in thermal accumulation within the ground and eventual system failure. The heat transfer performance of energy pile systems during long-term operation under unbalanced thermal loads must be investigated. Moreover, the design parameters of energy piles are usually constrained by the requirements of foundation structural design, resulting in energy piles being densely arranged. Hence, the influence of pile spacing on the heat exchange performence of energy piles must be comprehensively understood. In this study, two- and three-dimensional energy-pile heat transfer models were established and innovatively coupled based on an engineering project currently under design. Numerical simulations were performed to investigate the heat transfer behavior of energy-pile groups subjected to unbalanced thermal loads and the effect of pile spacing on their heat exchange performance. Furthermore, design recommendations regarding the determination of the proportion of thermal loads to be borne by the energy piles in a hybrid GSHP system were provided. The results indicate that the proposed 2D-3D coupled modeling approach is able to simulate the heat exchange performance of large-scale energy pile groups. Pile spacing considerably affects the long-term thermal performance of energy-pile groups, especially in cases with small pile spacings. The influence of pile spacing on the heat exchange capacity of energy piles can be considered in the design phase by incorporating a group effect coefficient η, which are calculated to be 0.165, 0.470, 0.732, and 1 for pile spacings of 2 m, 4 m, 6 m, and 10 m, respectively.