Abstract: Organic-rich shale is a significant potential source of oil and gas that requires development through in situ conversion technology. However, the evolution patterns of the internal three-dimensional (3D) pore structure and kerogen distribution at high temperatures are not well understood, making it difficult to microscopically explain the evolution of the flow conductivity in organic-rich shale at high temperatures. This study utilizes high-resolution X-ray computed tomography (micro-nano CT) to obtain the distribution of pores, kerogen, and inorganic matter at different temperatures. Combined with the pyrolysis results for the rock, the evolution of the pore structure at various temperatures is quantitatively analyzed. Based on three-phase segmentation technology, a model of kerogen distribution in organic-rich shale is established by dividing the kerogen into clustered kerogen and dispersed kerogen stored in the inorganic matter and the pores into inorganic pores and organic pores within the kerogen skeleton. The results show that the inorganic pores in organic-rich shale evolve through three stages as the temperature increases: kerogen pyrolysis (200–400 °C), clay mineral decomposition (400–600 °C), and carbonate mineral decomposition (600–800 °C). The inorganic pores porosity sequentially increases from 3% to 11.4%, 13.1%, and 15.4%, and the roughness and connectivity of the inorganic pores gradually increase during this process. When the pyrolysis temperature reaches 400 °C, the volume of clustered kerogen decreases from 25% to 12.5%. During this process, the relative density of kerogen decreases from 9.5 g/cm3 in its original state to 5.4 g/cm3, while the kerogen skeleton density increases from 1.15 g/cm3 in its original state to 1.54 g/cm3. Correspondingly, 7%–8% of organic pores develop within the clustered kerogen, accounting for approximately 50% of the volume of clustered kerogen. In addition, approximately 30% of the kerogen in organic-rich shale exists in the form of dispersed kerogen within inorganic matter, and its variation trend is similar to that of clustered kerogen, rapidly decreasing from 200 to 400 °C and stabilizing above 400 °C. The results of this study provide an essential microscopic theoretical basis for the industrial development of organic-rich shale resources.