The presence of water in narrow pore spaces affects the occurrence and flow of methane, which in turn affects shale gas production. Therefore, studying the occurrence and distribution characteristics of water is of great significance to predict gas production. Based on molecular dynamics simulations, this study investigated the occurrence characteristics and influencing variables of liquid water in kaolinite nanopores in situ. Owing to its widespread distribution, kaolinite is the most prevalent clay mineral with two surfaces with different characteristics. Three systems of pure water, a CaCl 2 solution, and a H 2 O/CH 4 mixed phase were created at varied temperatures (80−120 °C) and pressures (70−120 MPa). The presence of gas and water in the nanopores was investigated thoroughly. The results showed that the adsorption of water on the Al−O octahedral surface of kaolinite was not affected by external conditions under in situ conditions, whereas the adsorption of water on the Si−O tetrahedral surface decreased with increasing temperature, but the change was small. When ions were present in the system, the water capacity decreased. Based on the aforementioned results, external conditions, such as temperature and pressure do not affect the basic state of water. However, if there are more than two fluid types in the system, the adsorption of water on the mineral surface is reduced owing to competitive adsorption. In addition, a CH 4 −H 2 O mixed system was simulated, in which methane molecules were distributed in clusters. There are two types of adsorptions in pores: gas−solid interactions and solid−liquid−gas interactions. CH 4 molecules are thought to be clustered in water molecules because of the strong hydrogen bonding interactions among the water.