Marine organic-rich shales in southern China maintained overpressure conditions caused by hydrocarbon thermal cracking during the deep-burial stage and gas leakage during the period of tectonic uplift, accompanied by organic pore development and preservation. Presently, there is no comprehensive framework for revealing the preservation of organic pores in shale reservoirs. In this study, multiple approaches, including CO₂ and N₂ adsorption, scanning electron microscopy, fluid inclusion microthermometry, laser Raman spectroscopy, and thermodynamic modeling, were used to quantitatively evaluate organic pores and investigate pore fluid pressure evolution in the Wufeng Formation and Longmaxi Formation shale reservoir in the eastern Sichuan Basin. Measured results show that organic micropores in shale samples from three wells at different structural units have similar values of volume and specific surface area. Organic mesopore volume accounts for 40% to 70% of the organic pore volume. The degree of organic mesopores development in wells JYA, JYB, and JYC is proportional to the pressure coefficients (P_c) with shale reservoirs. Pore fluid pressure evolution within shale reservoirs can be divided into two stages: 160–85 Ma and 85 Ma to present day. Overpressure was generated in shale pores during the first stage, with P_c increasing from 1.57 to 2.2, and the overpressure protected most of the organic pores from compaction. The second stage was characterized as the reduction and dissipation of overpressure during the Yanshanian and Himalayan Orogenies. By comparing the closed-system modeling of overpressure and pore fluid evolution across different structural zones, this study demonstrates the possible increase in overpressure and decrease in organic pore volume during the Yanshanian Orogeny. In intensely tectonically active zones, the development of faults and fractures can lead to overpressure dissipation within shale reservoirs, resulting in poor organic mesopore preservation and low hydraulic fracturing productivity during the Himalayan Orogeny. Conversely, in weakly tectonically active zones, the shale reservoir maintained an overpressured state during the Himalayan uplift, with large-diameter and high-roundness organic mesopores preservation, indicating that overpressure during uplift can provide important preservation for organic mesopores. This contribution provides greater insight into organic pore preservation and shale gas enrichment in other tectonic settings around the world.