Ground-source heat pump (GSHP) systems using composite energy geostructures can efficiently transfer heat to soil and provide a high coefficient of performance (COP) for both cooling and heating, which has broad application prospects for energy saving in buildings. However, groundwater seepage in the soil can significantly affect the heat-transfer performance of a composite energy geostructure, thereby affecting the overall system performance. Therefore, this study establishes a numerical model of composite energy geo-structures considering groundwater seepage and investigates their synergistic heat transfer mechanism of composite energy geo-structures during summer. The results indicate that the heat transfer of composite energy geostructures is 60% higher than that of single energy piles under seepage conditions owing to the synergistic heat transfer of the energy pile and borehole. Groundwater seepage contributes to heat transfer in composite energy geostructures. When the seepage velocity reaches 60 m/a, heat transfer capacity increases by 1.39 compared to non-seepage conditions, while the temperature rise of the structure itself decreases by 25.32%. Under seepage, the upstream energy geostructures exhibit greater heat transfer with the soil than those downstream. The thermal influence area of the energy geostructures significantly reduced upstream and expanded downstream. This study guides the rational application of composite energy geostructures in regions with seepage.