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Recent studies show that the shale gas content and storage space are influenced by connate water, while it is unclear how connate water occurs in different nanoscale pores in high and overmature shales, and research concerning the occurrence characteristics and factors controlling connate water in overmature shale gas formations is scarce. In this research, overmature lower Paleozoic shale samples from southeastern Chongqing were selected for connate water distribution and factor analysis. The results show that connate water in the lower Paleozoic shale occurs in organic matter and clay minerals, mainly occurs in clay minerals and tends to form clay-bound water in clay minerals. The effect of the connate water content (CIW) on the inorganic nonmicropore (mesopore + macropore) surface area (SA) is greater than that on the organic nonmicropore SA. The CIW mainly affects the micropore structure parameters of clay minerals, and the total organic carbon (TOC) content is the main factor controlling the shale micropore structure. Connate water occurs in shale micropores and nonmicropores, and adsorption and filling states simultaneously exist and are distributed in <10 nm mesopores and 0.4–0.6 nm micropores; this distribution reduces the pore structure parameters of inorganic matter in shale, especially the nonmicropore SA. The effect of the CIW on nonmicropore SA and micropore pore volume (PV) in inorganic minerals is significantly greater than that of organic matter. Connate water mainly occurs in inorganic mineral pores and mainly occupies the mineral nonmicropore SA. Connate water significantly reduces the inorganic pore structure parameters, while its effect on organic pores is limited.
•Connate water mainly occurs in clay minerals and tends to form clay-bound water.•TOC and clay mineral contents have an obvious effect on nonmicropore SA and micropore PV.•Connate water occurs in micropore and nonmicropore, and exists in adsorption and filling states.•Connate water occurs mainly in mineral pores and mainly occupies the nonmicropore SA.•Connate water obviously reduces the pore structure of inorganic matter and has limited influence on organic pores.