The thermal effect caused by deep magma intrusion can not only accelerate the metamorphism of coal body, but also bring additional thermal field that changes the mechanical environment of coal seams, thereby affecting the permeability of coal seams. Different from shallow coal resources, deep coal resources are in a mechanical environment characterized by limited stress and strain. Thus, the thermal effect has a more significant influence on the distribution and permeability characteristics of deep coal seams. In this study, the evolution history of highly metamorphic coal seams in Yangquan mining area was analyzed, and the main effect of magmatic activity on coal seams was obtained. Based on the determined vitrinite reflectance data of typical mines in Yangquan mining area, the maximum paleotemperature was calculated by adopting the Barker’s method. Furthermore, the paleotemperature distribution in Yangquan mining area was summarized, and its relationship with the metamorphic degree was acquired. Then, a new permeability model considering the thermal strain was proposed to analyze the permeability evolution in deep coal seams at different ground temperatures. Finally, through a combination of the results of gas pressure and outburst number in Sijiazhuang Mine, Yangquan No. 5 Mine and Xinjing Mine, the influence of ground temperature on the gas outburst risk in Yangquan mining area was explored. The following conclusions were drawn: The maximum paleotemperature in Yangquan area can be 303 °C. In addition, the paleotemperature in the south is higher than that in the north of Yangquan mining area. The various temperatures at different depths bring about different degrees of thermal stress to different coal seams, leading to different strains. Under the fixed displacement boundary conditions in the deep, the coal seam folds and bends to varying degrees. Moreover, the difference in the ground temperature raises the a value of coal seams and lowers the permeability, which promotes the formation of gas-rich zones and increases the risk of coal seam outburst. The research results can help mines to make proper gas disaster prevention plan for different zones.