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The pore structure and pore water of deep shale gas reservoirs are unique. Their complex occurrence mechanism is the root cause of gas content variations, which restrict successful and economic exploration and exploitation. In this study, nuclear magnetic resonance experiments were performed to characterize the pore structure and pore water microscopic migration in deep shale gas reservoirs of the Wufeng–Longmaxi Formation in the Luzhou block. The pore structure particularity and its influence as well as that of pore water on gas occurrence are discussed here. The results show that total organic carbon (TOC) content has weak positive correlation with the proportion of micropores, negative correlation with the proportion of mesopores, and strong positive correlation with the proportion of macropores. These indicate that organic matter developed mainly macropores and micropores, while inorganic minerals produced mainly mesopores. The proportion of producible porosity is relatively low (11.81% on average), reflecting the poor pore connectivity in the studied deep shale. Both the proportion of macropores and the TOC content are strongly positively correlated with the proportion of producible porosity. Organic matter controls the pore connectivity of deep shale by controlling the development of macropores. The producible porosity correlates positively with total porosity, indicating that shale with high total porosity possesses high producible porosity. The pore structure at different burial depths (especially different beds) has significant differences, reflecting strong interlayer heterogeneity. Compared with the shallow Qiongzhusi Formation, the deep shale has lower porosity, smaller dominant pore size, poor pore connectivity, and similar T2 spectrum distribution. Mineral anti-compaction protection pores and reservoir fluid over-pressure are the key to the development of organic pores in deep shale gas reservoirs. When adsorbed gas converts to free gas, the gas-in-place will directly be affected by whether the deep shale gas reservoirs can provide enough storage space for excess free gas. After centrifugation, there was still considerable residual water in the studied deep shale, and available pores decreased with increase in water saturation. There was a negative correlation between gas content and water saturation, indicating that primary formation water has a vital influence on the occurrence and enrichment of shale gas. These findings provide a collective theoretical basis for accurate evaluation of deep shale gas reservoirs, which is significant for the commercial exploration and exploitation of deep shale gas. [ABSTRACT FROM AUTHOR]