The interaction between shale and various fluids is crucial as it modifies pore structures, which govern the effective development of shale gas and the geological storage of carbon dioxide in shale formations. In this study, samples from the Longmaxi Formation shale in Sichuan Basin of China were exposed to different fluids, including 6 MPa CO2, 12 MPa CO2, 6 MPa CO2+brine, and 12 MPa CO2+brine, at 45 °C for 100 days. Various methods, including X-ray diffraction (XRD), X-ray fluorescence (XRF), field-emission scanning electron microscopy (FESEM), and the low-pressure gas adsorption (N2) test, were adopted to evaluate chemical and structural changes during the exposure process. After being treated with supercritical CO2+brine and subcritical CO2+brine, the shale underwent significant changes in its major element composition. The content of Ca, Al, and K in shale saturated with supercritical CO2+brine decreased from 13.00% to 10.34%, from 3.65% to 3.36%, and from 1.56% to 1.37%, respectively. Meanwhile, the content of Si and Na in the same shale increased slightly after saturation. The amount of quartz and dolomite increased, while the levels of clay and calcite slightly decreased. The surface of the shale sample became rougher and small bumps and cracks appeared after saturation with different fluids, as shown by the FESEM analysis results. Furthermore, the changes in both the total pore volume and pore size followed a similar pattern to the alterations in the specific surface areas. The highest level of variation occurred with the shale that was saturated with 12 MPa of CO2, indicating that gas pressure and CO2 phase state have a significant influence on the shale’s pore structure. In addition, the distribution of pore sizes showed a bias towards larger sizes across all diameters; this suggests that the reaction resulted in a decrease in the number of micropores. This also highlights that the impact of varying fluid saturation was primarily focused on micropores and macropores. The results of this study provided experimental evidence to further test the mechanisms and permeability of geological storage of CO2 in organic-rich self-sourced shale.