The origin of CO2 and the alteration of CO2 into clay minerals in eastern Shijiutuo symon fault of Bozhong Depression were studied in this paper. The elevated δ13C and R/Ra values show the mantle-derivation of CO2. The basin-controlling deep fault was the main migration pathway of CO2 fluid. CO2 fluid injection had obvious impact on clay minerals. CO2 late injection caused obvious thermal fluctuation and brought out the result that the montmorillonite of the illite/montmorillonite mixing layer was 15%~30% lower than that of mudstone at the nearby depth. The CO2-bearing reservoir bed was characterized by high authigenic kaolinites and low illite, which played a decisive role in reservoir quality improvement.