With the increase of mine mining depth, the dangerous gas mine is outstanding increasingly, and the risk factors affecting coal seam mining is becoming more and more complex. Protective layer mining is widely used in the currently regional technical measures to prevent coal and gas outburst, and many domestic coal mines have adopted mining protective layer to prevent the mine coal and gas outburst, and to realize the coal and gas outburst coal seam outburst elimination. In the protective layer, under the influence of working face mining stope, overburden will have corresponding deformation. The original stress state balance will be destroyed, leading to the permeability of coal and rock. Then, the intensity and gas pressure will be changed. This paper applies the numerical simulation software to simulate, the protective layer of roof strata after mining under unloading, coal strata movement deformation and fracture of rock mass and coal seam gas extraction methods for pressure relief system research. Mining protective layer is combined with the corresponding gas drainage measures for prevention and treatment of deep coal seam gas outburst, and the realization of coal mine safety production is very important.