• Zoning operation of energy piles is investigated to alleviate soil thermal imbalance. • Dense heat injection into the central piles can relieve the cold accumulation. • Heat extraction from the outer layer piles can relieve the cold accumulation. • A reasonable strategy is proposed to achieve good system efficiency and reliability. Energy piles have attracted increasing interest for application in ground source heat pumps, because it is environment-friendly, energy-efficient, and without additional drilling cost. However, when there is a large difference between the heating and cooling loads, the system will suffer from a soil thermal imbalance which may further decline the system performance and even cause a system failure. A hybrid ground source heat pump system that integrates auxiliary equipment can solve the problem, however, it needs additional investment and a complicated control strategy. In this paper, the zoning operation of energy piles can effectively improve the temperature recovery ability of soil in the energy pile group and thus alleviate the soil thermal imbalance. Specifically, a heating-dominated residential building in Beijing is selected for a case study, with 144 energy piles arranged in a 12 × 12 layout. An analytical model of the spiral-coil energy pile group with seepage will be adopted, which can consider the groundwater flow, the geometry of spiral coils, and the thermal interaction among different energy piles, achieving high calculation accuracy and fast calculation speed. Based on this analytical energy pile model, a system model will be built to investigate the system performance influenced by different zoning operation strategies. Results show that intensive heat injection into the center of the pile group (Strategy 2 and Strategy 3) or heat extraction from the outer layer of the pile group (Strategy 4) can relieve the cold accumulation. Strategy 2 can relieve the outlet temperature decline from 5.54 °C to 4.46 °C and improve the heating COP from 3.297 to 3.423 compared to the conventional full operation strategy. Although the annual heat pump COP of Strategy 2 is a little lower than that of conventional full operation strategy, Strategy 2 has the shortest unmet heating or cooling time. Therefore, the proposed zoning operation strategy can achieve good system efficiency and excellent system reliability compared to the conventional strategy.