The ground source heat pump systems with spiral-coil energy piles are promising for building energy saving in high-density cities. However, when applied in heating-dominant buildings, the soil thermal imbalance causes soil temperature decrease and heating performance degradation in long-term operations. To analyze the effect of different influential factors on the soil thermal imbalance, an analytical model for spiral-coil energy pile group under seepage conditions is proposed, considering different heat fluxes of piles and time variation of heat fluxes. A sandbox experiment is used to validate the proposed model, based on which a system model is further established to investigate the long-term performance ground source heat pumps. Results show that (1) the energy piles in the outer layers of the group, at the upstream of the seepage flow direction, with a large pile spacing, or arranged in a line shape exchange more heat with soil; (2) the groundwater effectively alleviates the temperature decreases of soil near the energy piles and located at the upstream; (3) the groundwater flow, a slim pile layout, a large pile spacing, and a short pile length are effective to alleviate the decreases of the outlet fluid temperature and heating efficiency, contributing to higher heating capacities and lower energy consumptions.