The Qinshui Basin is located in the southeast of Shanxi Province, China. It is one of the most abundant coal resources from Permo-Carboniferous North China. It is rich in coal and coalbed methane resources. However, the accumulation of coalbed methane is complex and the enrichment law has not been fully understood because of the high heterogeneity of coal reservoirs in the Qinshui Basin. The examination of dissimilarities between tectonically deformed coals (TDCs) and primary coals at multiple scales holds paramount importance in advancing our understanding of the occurrence and flow patterns of coalbed methane, and in providing guidance for exploration efforts. In the present study, the samples from the Jincheng Mine, Qinshui Basin, were studied by X-ray diffraction (XRD), scanning electron microscopy (SEM), mercury intrusion porosimetry (MIP), CO2 gas adsorption and 3D X-ray micro-computed tomography. The results showed that the dominant minerals in coal were illite, kaolinite, and calcite, with minor amounts of quartz and ankerite. In comparison to primary coal, tectonism could increase the microfractures density of type A (the fracture of width ≥ 5 μm and length > 10 mm) in TDCs. In CO2 gas adsorption in mylonite coal, it was observed that the volume of micropores (<2 nm) was significantly reduced leading to a decrease in gas adsorption capacity. The result of Micro-CT scanning revealed that the minerals occurred as veins in primary coal, but as irregular aggregates in TDCs. Moreover, tectonism had a staged impact on fracture structure, which was initially closed in cataclastic coal and then formed into granulated coal during the tectonic evolution. The effects of tectonism on coal structure had an impact on the connectivity of micropores at the micrometer scale by the destruction of the pore throat structure, increasing the heterogeneity of the reservoir. These findings help to better understand the changes in TDC structure at different scales for developing effective strategies for coalbed methane exploration and production.