Geothermal energy in hot dry rock formations is an important component of China’s geothermal resources, and its development is of significant importance for achieving the "dual carbon" goals. The reservoir rocks of hot dry rock formations are mainly granites. The lithology of granites is dense and is usually developed by Enhanced Geothermal System (EGS). As the main pathways for fluid flow and heat transfer in the circulation process, both artificial and natural fractures deformation can lead to the evolution of conductivity, thereby influencing the heat extraction performance of the thermal reservoir. Existing studies on conductivity mostly focus on artificial fractures, often centered around matrix elastic deformation, without considering the impact of natural fractures damage. To reveal the effects of natural fractures damage, a high-temperature and high-pressure rock core injection and extraction multi-field coupling experimental platform is independently developed and designed. The reliability of the experimental system was analyzed and verified, corresponding experimental schemes and procedures are designed. Natural fractures were used to penetrate the rock samples, study the variations of injection and extraction differential pressure with injection flow and confining pressure at room temperature. The characteristics of natural fractures damage at high temperatures were analyzed, and the impact of natural fractures damage on the evolution of conductivity under different injection flow, temperature difference and injection modes were compared. The experiments demonstrated that injecting cold fluid resulted in a significant increase in the volume of natural fractures compared to the initial state, primarily through weak cementation failure damage. Under no confining pressure conditions, damage caused an increase in fracture aperture and length, enhancing fracture connectivity and altering fracture conductivity. Therefore, natural fractures should be considered in the design of fracturing and heat extraction schemes. The injection and extraction differential pressure increased with increasing confining pressure and injection flow, with a maximum increase of up to 0.6 MPa. During high-temperature production, the maximum changes in injection and extraction differential pressure and conductivity evolution rate reached 1.11 MPa and 26.59%, respectively. Characteristics of fracture damage are more pronounced under higher injection flows and temperature differentials. Fracture damage is more significant under intermittent injection compared to continuous injection. Grey relational analysis identified the primary controlling factor as the temperature differential, indicating that thermal stress is the main cause of additional conductivity evolution due to fracture damage. This study highlights the necessity of analyzing natural fractures damage in the long-term production process of hot dry rock formations, providing valuable guidance for engineering field construction.