Kerogen molecular structure controls the micropore (<2 nm diameter) evolution in shale and exerts a significant impact on shale gas adsorption, desorption, and diffusion. However, the influence of tectonic deformation on kerogen structure and organic micropores needs intensive study. Our study mainly focuses on the transformations in the extracted kerogen structure and organic micropores of Longmaxi shale during tectonic deformation. Vitrinite reflectance measurement (VRM) and Raman spectroscopy (RS) were utilized to determine the maturity of organic matter. Organic pore network attributes of kerogen samples were estimated using CO2 adsorption experiments. High-resolution transmission electron microscopy (HRTEM), Fourier transform infrared spectroscopy (FTIR), and 13C nuclear magnetic resonance (13C NMR) were utilized to interpret the kerogen molecular structures of these samples. VRM and RS results show that Longmaxi shale has reached the wet gas window. Adsorption analyses of CO2 indicate that kerogen samples in shale with strong deformation have larger micropore volume and surface area (<2 nm). 13C NMR and FTIR results reveal that the tectonic stress may promote the shedding of aliphatic carbon. HRTEM images exhibit that aromatic rings with a size of 3 × 3 account for the largest proportion in all kerogen samples, which indicates that the kerogen samples have reached a high thermal evolution level, consistent with the Raman experiment. For weakly deformed shale samples, 66.5 and 88.8% of the total number of aromatic rings in LZ-1 and LZ-4 kerogen belong to the major direction (within a 45° range). In the most strongly deformed sample, LZ-2, distribution orientations of aromatic fringes are dispersed and primarily concentrated at 15–105°. Such disorientation of nanometer-sized polyaromatic layers in the strongly deformed sample creates a nanopore network in organic matter (OM) that increases the micropore volume and surface area. These findings from integrated approaches can provide a new perspective of adsorbed gas enrichment in the complex tectonic areas.