The deformation process of the coal bodies is recorded by the friction surfaces widely developed within tectonically deformed coals (TDCs), and gas occurrence within coals is significantly influenced by their surface molecular structures. Therefore, profound theoretical significance for coal mine gas safety is held by the investigation into the structural evolution of these friction surfaces and their surface structure. Through the comprehensive utilization of various molecular structure characterization techniques and molecular dynamics simulations, the evolution characteristics and mechanisms of molecular structures on the friction surfaces of TDCs are systematically investigated. It is indicated by the results that with the enhancement of shear friction, the development degree of secondary structural defects within the organic matter on the surface layers of the bodies of coals is reduced under the synergistic effect of stress and frictional heat. Concurrently, the content of less stable heteroatom functional groups is decreased, the directionality of lattice fringes is enhanced, and the length of lattice fringes, the size of aromatic clusters, and the relative molecular weight are all increased, by which the degree of graphitization is continuously elevated. Distinct stage-by-stage differences are exhibited during this evolutionary process. Specifically, during the stage from primary joint surfaces to striated mirror-like friction surfaces, the rapid healing of secondary structural defects is driven by the frictional thermal energy generated via rapid shear friction, through which a large amount of heteroatom functional groups is degraded. Furthermore, a dominant position is occupied by the condensation of short lattice fringes into medium-length fringes, while no significant improvement is achieved in the directionality of lattice fringes. In contrast, during the stage from striated mirror-like friction surfaces to wavy mirror-like friction surfaces, a slowdown in the growth rate of defect healing and functional group degradation for organic molecules on the friction surfaces is induced under the action of intense shear stress or strain energy. Meanwhile, the orderliness of lattice fringes is significantly increased, and an evolutionary pattern dominated by the condensation of medium-length lattice fringes into long lattice fringes is ultimately formed. The evolutionary mechanism of organic matter on the surface layers of the friction surfaces of TDCs is revealed from a molecular scale by the research results, through which a novel perspective is provided for a profound understanding of the mechanisms of coal and gas outburst, as well as disaster prevention and control.