Abstract: Geothermal resources are abundant in deep mines. Functional backfill technology combines deep mining and deep geothermal mining to achieve a win-win situation for mineral and geothermal resource development and is an important measure for extending the life of deep mines. In this paper, on the basis of an analysis of the research status of geothermal resource extraction through tubes embedded in backfill bodies in mines, a horizontal square-spiral-type backfill heat exchangers (S-S BHE) is proposed. Considering the significant influence of groundwater advection on the heat extraction of backfill heat exchangers (BHE) in mines and the relative scarcity of previous studies, a verified three-dimensional unsteady BHE model coupling heat transfer and seepage are established using COMSOL software. Based on this model, a mathematical model of the backfill heat exchanger coupled heat pump (BHECHP), and four comprehensive evaluation indicators are established. Firstly, the performance of the S-S BHE is compared with that of two typical serpentine BHEs under the same geometric and physical conditions. The results show that the S-S BHE performs better than the two serpentine BHEs across the board, and the advantage is more substantial under situations of higher permeability flow. Secondly, the characteristics of the S-S BHE and its coupled heat pump are examined in relation to the in-tube flow rate, tube spacing, seepage velocity, and inlet water temperature. The in-tube flow rate and seepage velocity are found to have the most significant effects on the comprehensive evaluation indicators. The average heat transfer power per unit of tube length increases with flow rate, but the heating seasonal performance factor (HSPF) decreases obviously. The analysis revealed an optimum interval of 0.4–0.6 m·s^?1 for the flow rate in the tube, where the flow of circulating water in the tube is in transition from the transition zone to the fully turbulent flow zone. The effect of seepage velocity is negligible at less than 10^–6 m·s^?1, and all comprehensive evaluation indicators present linearly increasing trends in the usual seepage range of 10^–6 to 10^–5 m·s^?1. Finally, an ecological evaluation of the S-S BHECHP was conducted. A comparison with traditional heating methods reveals that the heating method using S-S BHECHP has a significant energy saving and carbon reduction effect. The primary energy consumption and carbon emissions of the S-S BHECHP are reduced by 83.39%, 61.57%, and 56.84% compared to the regenerative electric boiler, coal-fired boiler, and air-source heat pump, respectively. The findings of this study show how well the S-S BHE and the S-S BHECHP performance, and they also provide some theoretical recommendations for the application and exploration of heat storage/energy storage functional backfill in deep mines.