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The increasing emission of carbon dioxide (CO2) has promoted the development of Carbon Capture and Storage (CCS) as a climate change mitigation strategy. The Kujung Formation is considered a potential carbonate reservoir for geological CO2 storage. This study evaluates the geochemical evolution of CO2 storage in the Kujung Formation using TOUGHREACT and its effects on mineral alteration and reservoir petrophysical properties. A coupled reservoir–caprock system was simulated over a 100-year period, while a full factorial Design of Experiments (DoE) was applied to evaluate the effects of reservoir temperature and CO2 injection rate. The results show that calcite and illite were predominantly controlled by precipitation, whereas dolomite, kaolinite, quartz, and muscovite were dominated by dissolution. These mineral alterations resulted in slight increases in reservoir porosity and permeability, both by approximately 0.24%. In contrast, the caprock exhibited only minor changes, with porosity increasing by approximately 0.05% and permeability by approximately 0.10%. Sensitivity analysis revealed that reservoir temperature had a greater influence on geochemical evolution than CO2 injection rate. Overall, the results demonstrate the important role of geochemical reactions in controlling mineralogical evolution and petrophysical changes during geological CO2 storage.