In order to deeply investigate the influence of rough fracture seepage heat transfer characteristics in the fractured rock body, the influence of fracture morphology on the temperature distribution was investigated by 3D scanning of the rough fracture surface after Brazilian splitting, decomposing and reconstructing the extracted two-dimensional rough contour using wavelet decomposition, and convective heat transfer simulation of the fracture with different roughness levels, the influence of the fracture morphology on the temperature distribution was investigated, and the rough profile factor RPF was proposed to correct the flat plate model-derived. The roughness profile factor RPF was proposed to correct the heat transfer coefficient derived from the flat plate model, and the composite factor CF was used to represent the morphological characteristics of the decomposed rough single fracture profile, and the influence of the rough fracture characteristics on the heat transfer of the flow was investigated. The results show as follows. The increase of secondary roughness makes the local temperature fluctuate greatly, promotes the generation of thermal convection, and enhances the heat transfer effect. The modified heat transfer coefficient takes into account the influence of the rough profile of the slit, and the fitted expression given fits well with the results. Too large aperture diameter attenuates the influence of the rough profile, which results in the decrease of the heat transfer efficiency and the outlet temperature, and the growth of h slows down after exceeding the critical CF value. As CF increases, the outlet temperature shows a decreasing trend, indicating that pore size and roughness have a significant effect on the improvement of heat transfer capacity.