Abstract: The heterogeneity of coal microdeformation has a significant impact on the occurrence and migration of coalbed methane, and the difference in organic maceral deformation is the key to analyzing coal microdeformation. To date, there are few studies on the inner relationship between the deformation differences of organic macerals and their mechanical properties and molecular structure. Therefore, based on the study of the deformation differences among organic macerals in tectonically deformed coal, this study verified the deformation law of organic macerals under the in-situ temperature and stress through the physical simulation experiments involving high-temperature and high-pressure deformation of primary structure coal. Combined with the test results of in-situ nanomechanical parameters and molecular structure characteristics of each organic maceral, this study reveals the mechanical basis and molecular structure essence of the deformation differences in organic macerals of tectonically deformed coal, as follows. Exinite has the lowest hardness, elastic modulus, and maximum creep displacement because its molecular structure is loose with low stability and the minimum stress resistance, thus, exinite tends to produce ductile bending deformation under tectonic stress. The molecular structure of vitrinite is relatively tight with higher stability and larger stress resistance, thus, vitrinite has higher hardness, elastic modulus, and smaller creep displacement, and easily appears to brittle fracture deformation under stress. In comparison, the molecular structure of inertinite is the most compact with the highest stability and maximum stress resistance, and inertinite shows the highest hardness, elastic modulus, and minimum creep displacement, so that inertinite has weaker brittle fracture deformation than vitrinite under the same tectonic stress.