CO2 storage in deep reservoir is an efficient way to mitigate climate change. The carbonate reservoir is one of the selected storage sites but which is sensitive to the acidic environment, where the CO2 saturated formation water could be as medium acid in the reservoir condition and hence change the microstructures. However, the capillary trapping mechanism is highly corrected with such microstructures. Thus, fully understand such CO2-water-rock interaction and the related capillary trapping change are very important for the storage security issues. In this paper, we microCT imaged the microstructure change of oolitic limestone sample due to CO2 saturated brine injection, and calculated the capillary pressure based on the fractal theory. We found that the calculated capillary pressure decreased after live brine flooding which indicated a CO2 capillary trapping loss and such calculated capillary pressure change was also highly corrected with the morphology of the dissolved matrix area.