With the depletion of shallow mineral resources, the sustainable development and utilization of deep mineral resources will become a normal activity. As a type of clean energy to promote sustainable development, gas in deep coal seams has attracted wide attention. A better understanding of the permeability evolution induced by mining disturbance and the geological environment is of great importance for underground coal exploitation and gas extraction. In order to analyze the evolution of the mechanical properties and permeability of deep coal that are induced by high ground temperature, coal of the Pingdingshan Coal Mine has been investigated, and the seepage tests were carried out by keeping the confining pressure constant and loading and unloading axial stress under different temperature conditions. The effect of temperature on the peak strength and the initial elastic modulus of coal samples is analyzed. The evolution of permeability, which is estimated with the transient pulse method, based on fractional derivative and fracture connectivity, are discussed by establishing the relationship between fracture connectivity and fractional derivative. Meanwhile, the damage variable that is caused by stress and temperature is introduced and the contribution of thermal damage on coal damage accumulation is discussed. A theoretical model is proposed regarding permeability evolution with temperature and stress based on the Cui–Bustin model, which is verified by experimental data. It has been found that the strength and elastic modulus of deep coal decrease nonlinearly with increasing temperature, which demonstrates that temperature has a weakening effect on the mechanical properties of coal. The fracture connectivity and permeability evolution trends with axial strain are consistent under different temperatures, which decrease slowly in the compaction and linear elastic stages, reach the minimum at the volumetric dilation point, gradually increase in the yield stage, then have a sharp increasing trend in the post-peak stage and, finally, become steady in the residual stage. The damage induced by temperature increases with rising temperatures under different external load conditions. When the external load increases gradually, the thermal damage still accumulates, but the thermal damage variable ratio decreases. The proposed permeability model considering temperature and stress can describe the trend of the experimental data. With axial stress increasing, the influence of temperature on permeability decreases, and its leading effect is mainly reflected in the compaction stage and the linear elastic stage of coal.