To study the influence of CO2 on the structure of a coal reservoir during CO2 geological storage-enhanced coalbed methane recovery (CO2-ECBM), two high rank coals from the Qinshui basin were exposed to supercritical CO2 (ScCO2) and water for 240 h in a laboratory high-pressure supercritical geochemical reactor to simulate the reaction of ScCO2-H2O-coal under three burial depths. The changes in the chemical structure of the coals before and after reaction were evaluated by Fourier transform infrared spectroscopy (FTIR). The results show that the ScCO2-H2O treatment has a substantial influence on the coal structure, reducing the aromaticity and the degree of aromatic ring condensation, increasing the hydrocarbon-generating potential and improving the maturation level of the coals. The ScCO2-H2O system mainly affects the organic functional groups of coals through the chemical reactions: swelling effect, bond dissociation reaction, hydrolysis and substitution reaction. The results of peak fitting show that the ScCO2-H2O treatment can significantly reduce the intensities of the bands associated with in-plane -CH2- vibrations and oxygenated groups (especially C-O groups), but increase the intensities of the aliphatic hydrocarbon and hydroxyl group bands. The changes in the functional group contents after the ScCO2-H2O treatment varied between the different rank coals. The effect of temperature and pressure on the functional group contents after reaction is complicated, and it is affected by the macromolecular structures of the raw coals and the sensitivities of the chemical reactions to temperature and pressure. However, there is a critical depth that provides the optimum influence of temperature and pressure on the structure of the organic matter in coal. This paper aims to provide a theoretical foundation for the study of the changes in the coal matrix structure during the long-term storage of CO2 in coal seams.