The evolution of fissures and permeability associated with mining of the upper protective layer of the coal seam is crucial for pressure relief gas drainage of the underlying seam. To understand the influence of mining the upper protective layer on gas drainage within the underlying coal seam, this study utilized the M16 and M18 seams in the Qinglong Coal Mine in Guizhou. Theoretical analysis, discrete element numerical simulation, and field tests were used to characterize the evolution of fractures associated with mining of the upper protective layer and the effects of pressure relief gas drainage within the protected coal seam. The results show that mining-related stress changes controlled the development of fractures, altering the permeability values of coals. An analysis of the crack development in the coal mass caused by mining of the upper protective layer shows that during the initial stage of mining, the produced cracks exhibited a butterfly shape network. Yet, with further development of the mining, these cracks and the stress changes gradually produced an inverted butterfly shape network. According to simulations, the areas of maximum deformation via expansion in the protected coal seam were located near the open cut and the mining end line of the working face. The maximum deformation values were 29.06 and 26.68 mm, respectively, and the corresponding deformation rates were 9.37‰ and 8.61‰, which are greater than the required 3‰. The findings of this study provide a new reference for gas control in pressure relief coal seams under similar working conditions.