Abstract: The geological sequestration of CO₂ in coal seam is a most promising carbon storage technology, which can help achieve the dual goals of CO₂ emission reduction and coalbed methane stimulation. Compared with other sealing geological bodies, coal has extremely well-developed micropores. The mechanism of geological sequestration of CO₂ in coal seam is closely related to the interaction of coal-gas-water. However, its internal influence mechanism is still unclear. Herein, the models of macromolecular structure and plat pore of the coals were constructed based on the systematic coal petrological analysis and testing of two bituminous coal samples. Meanwhile, the wetting behaviors of CO₂ and water on different coal-matrix surfaces at different temperatures and pressures were simulated using the molecular dynamics method. Thereby, the change rule of water wettability caused by the injection of CO₂ in coal seam was disclosed, and the influencing factors and microscopic mechanisms of injectability, storage potential and storage effectiveness of CO₂ in coal seam were preliminarily clarified. The results show that: (1) The main factor affecting coal wettability is the polar oxygen-containing functional groups in coal. Specifically, the higher the content of the oxygen-containing functional groups, the stronger the wettability of coal is. (2) The CO₂ injected into coal penetrates the water molecular layer through dissolution, and thus a competitive adsorption occurs with the water molecules, weakening the wettability of water on the coal surface. (3) With the increase of pressure and the decrease of temperature, the more CO₂ is adsorbed on the coal surface, and the more obvious the destruction of hydrogen bond and the decrease of wettability. (4) The hydrophilic coal seam has relatively poor injectability and storage potential of CO₂, but relatively good storage safety. (5) The CO₂ storage potential of coal seams are mainly influenced by the capacities of adsorption trapping and capillary trapping, while the effectiveness and security of storage are affected by the capacities of capillary trapping and structural trapping. (6) The sequestration of CO₂ in coal seam is mainly related to the adsorption trapping, taking capillary trapping under water-bearing conditions into account. The storage potential of high rank coal is higher than the low rank coal, but the “water block” effect needs to be overcome during CO₂ storage and injection. Moreover, the further study was conducted for the interaction of coal-gas-water and the geological sequestration mechanism of CO₂ in the deep coal seam under the in-situ conditions, which is of great significance for the development of CO₂-ECBM technology.