Organic‐rich shales, deposited in marine‐continental transitional environments, are widely distributed in southern China. The pore evolution of the Late Permian Longtan Formation shale (Guizhou Province) during its diagenesis and organic matter (OM) evolution was quantitatively and qualitatively investigated through thermal simulation, mercury intrusion capillary pressure, gas adsorption, fractal dimension, and field emission‐scanning electron microscopy observation. Diagenesis and OM evolution stage were subdivided on the basis of X‐ray diffraction, rock pyrolysis, and vitrinite reflectance test; moreover, the main controlling factors of pore structure during evolution were also discussed. Shales were heated to different temperatures with their vitrinite reflectance ranged between 1.23% and 3.12%, indicating that organic matter had evolved from a low‐ to a post‐mature stage. According to the changes in clay mineral composition, hydrocarbon generation, and Tmax, we subdivided diagenesis into four parts, each of which has a good correspondence with OM evolution. Pore volume (PV) varied between 0.012162 and 0.033482 cm3/g, while the specific surface area (SSA) varied between 13.3693 and 23.0094 m2/g. Mesopores were the main contributors to the total pore volume, while mesopores and micropores were the main contributors to the total specific surface area. In this study, the evolution of pore structure was not monotonous, but intermittent: The PV and SSA of shale samples first decreased and then increased. Maturity was the most important factor affecting the evolution of pore structure. The abundance of pores in OM, associated with hydrocarbon generation, resulted in large micro‐PV and micro‐SSA; moreover, the composition of clay minerals also influenced the pore structure evolution. The transformation of kaolinite into illite increased the content of illite and illite/smectite mixed layer, hence affecting the overall meso‐PV and meso‐SSA.