The natural fracture system present in coal provides the principal channel for transporting coalbed methane. Dissolving or modifying mineral occlusions has the potential to enhance the permeability of highly mineralized coal seams. In this study, low-rank mineralized coal was examined using x-ray computed tomography (CT) scanning. A novel in situ demineralization method based on coal CT images was developed using an improved pore-scale three-dimensional morphological modeling algorithm to further investigate the effect of mineral alteration on the dynamic evolution of microstructure and seepage characteristics. The results indicate that the development of pore-fracture and the alteration of mineralogical properties affect the demineralization work. Demineralization increases the connected porosity from 4.16% to 15.42%, significantly increasing the interconnected pore space of the coal. Meanwhile, permeability improved from 0.73 to 2.15 μm2, and a 194.5% increase after the completion of the demineralization work. A higher demineralization degree can develop the preferential flow channels well, resulting in a more rapid pore pressure drop. As demineralization progresses, the flow streamline distribution becomes more homogeneous, and new flow channels emerge. The proposed method shows superior performance in poorly connected areas, with a 69.29% higher permeability compared to previous methods.