To elucidate the role of effective pore preservation in controlling shale gas enrichment and high yield. This study focuses on fine-grained sedimentary shale of the Qiongzhusi Formation in Sichuan Basin, sampled from different tectonic settings. Rock facies were classified based on total organic carbon (TOC) measurements, X-ray diffraction (XRD), and cast thin section observations. The same lithofacies shale was selected for multi-scale pore characterization and field emission scanning electron microscopy (FE–SEM) to identify pore types and pore structures. By integrating actual drilling and logging data, paleopressure reconstruction via methane inclusion Raman spectroscopy, and burial history analysis of gas reservoirs, the preservation conditions of gas reservoirs are clarified. This study systematically reveals the mechanisms of shale pore preservation at different tectonic settings under the coupled effects of mineral composition, sealing systems, and fluid overpressure. A conceptual model for pore preservation in the Qiongzhusi Formation shales is further proposed. The results show that the deep shelf shales within the rift trough is characterized by high TOC, a rigid mineral skeleton, and overpressure storage. These shales develop an organic–inorganic composite pore network, exhibiting significantly higher pore volume and gas yield compared to shales outside the trough. At the trough margin, a semi-closed system with plastic mineral framework and moderate overpressure supports medium porosity. In contrast, shales outside the rift trough exhibit the weakest pore preservation capacity due to an open system, normal pressure, and plastic mineral framework. This study proposes a ternary synergistic pore preservation model of “rigid skeleton–closed system–hydrocarbon fluid overpressure”, which provides critical geological insight for the exploration and development of deep fine-grained sedimentary shale gas.