One of the most effective methods for geothermal energy extraction in deep mine stopes is the installation of heat exchange tubes within cemented backfill bodies. However, the complex underground environment can cause fracture in the backfill, which may negatively affect the geothermal extraction performance, especially in the presence of groundwater flow. This study establishes a three-dimensional seepage and heat transfer coupling model of cemented backfill heat exchangers with horizontal penetrating rough fractures via a finite element software platform. The model employs the Monte Carlo method combined with linear filtering to generate a rough fracture. The findings demonstrate that for fracture apertures ranging from 0 to 0.3 mm, the predominant mechanism of heat transfer is thermal conduction, with a negligible contribution from groundwater flow. However, as apertures expand from 0.3 mm to 2 mm, groundwater flow significantly enhances heat transfer, stabilizing beyond 2 mm. Increased fracture roughness at a 0.2 mm aperture does not enhance the heat recovery performance of the heat exchange tubes, but at a 4 mm aperture, a strong positive correlation between roughness and heat transfer is observed. Thus, narrow fractures can be treated as smooth, whereas roughness must be considered for wider fractures. The interaction between fracture flow and Darcy seepage increases with increasing groundwater hydraulic head, resulting in a notable improvement in the heat extraction performance of the heat exchange tube. When the relative position transitions from 0.75 °C to 0 °C, the outlet water temperature of the heat exchanger tube increases by approximately 9 °C.