Alternating layers of sandstone and shale were established. According to the permeability values, the lithology of the sandstone layer was classified, and a multiple lithofacies model was built to investigate the heterogeneity. The distribution of CO₂ injected into deep saline aquifers composed of alternating layers was simulated using TOUGH2/ECO2N software, which was often used to simulate multi-component and multi-phase flow. The results show that CO₂ accumulated in the bottom of the low-permeability shale layer and showed a layered structure. CO₂ preferred to migrate in highly permeable rocks and was distributed dispersedly in the sandstone layer. The supercritical CO₂ dissolved in the formation water continuously, and the density of the salt water consisting of saturated CO₂ increased, leading to the gradual subsidence of the salt water. No significant stratification was found.