Methane adsorption/desorption not only causes coal matrix shrinkage and swelling, but also has an important influence on the microcrystalline structure of coal. In this study, high-pressure isothermal adsorption/desorption experiments were carried out for 8 coal samples with different degrees of metamorphosis. The microcrystalline structure of the samples before and after methane adsorption/desorption were quantitatively examined using X-ray diffraction, high-resolution transmission electron microscopy, and laser Raman spectroscopy. The results showed that after methane adsorption/desorption, the interplanar spacing (d(002)) of the coal samples increased, and the unit stacking height (Lc) and unit lateral size (La) of coal crystallites decreased as compared with the raw samples. The changes in Lc were greater than those in La for the same sample. In other words, deformation from high-pressure adsorption/desorption has an especially significant impact on Lc. Furthermore, the fringe spacing of the samples increased, and the proportion sized 0.36-0.40 nm increased in the frequency histogram. While the fringe length showed a decreasing trend, the proportion in the range of 0.30-1.00 nm was significantly increased in the frequency histogram. In addition, the D peak positions of the samples increased while those of the G peak decreased, and their difference decreased. Moreover, the full widths at half maximum of G and D peaks, and the area ratio between D and G all increased. These results are of great significance for further understanding the source of excess coalbed methane (CBM) and its state.