Natural or hydraulic fractures in enhanced geothermal systems (EGS) typically have complex void structures due to the presence of surface contact. In this study, fluid flow and heat transfer processes in three-dimensional rough fractures with different contact ratios are investigated. Stronger flow channeling and heterogeneous heat transfer are observed in fracture voids with increasing surface contacts, and the fluid flow exhibits nonlinear characteristics due to the complex fracture void structures. Parts of fracture voids with large apertures and void areas contribute negligibly to the overall flow due to their weak connectivity to the main flow channels. Removing the low-flow regions does not significantly impact the flow channeling and heterogeneous heat transfer in the fracture voids. However the heat exchange in the low-flow regions results in differences in the overall heat transfer coefficient and heat extraction rate between the reconstructed and original fractures. An empirical model is proposed to describe the overall heat transfer coefficient in fractures with complex void structures. Furthermore, the flow and heat transfer processes in the highly contacted fractures are not significantly affected by the change in flow direction, indicating that the anisotropic degree of the fracture void structures decreases as the contact areas increases. This study may further deepen the understanding of fluid flow and heat transfer in realistic fractured rocks at high temperatures, which is critical for geothermal energy extraction.