This study experimentally investigated the impact of CO2 miscible flooding on oil recovery and alteration of rock properties in two carbonate cores consisting of more than 98% calcite: Edwards white representing a homogenous medium mainly consisted of micropores, and Indiana limestone representing a heterogeneous medium mostly composed of macropores. Several methods were applied to investigate the alteration of rock properties by CO2-water-carbonate minerals interactions: 1) Core flooding to measure overall changes, 2) MICP and X-ray CT to analyze small pores and large pores, respectively, 3) SEM, PCM, and ICP to verify physical and chemical reactions. Oil recovery was higher in Edwards white than in Indiana limestone, since characteristic of Edwards white contributes to sufficient contact time and stable displacement between oil and CO2. From the analysis of the alteration of rock properties in homogenous sample, dissolution facilitates the enlargement of pore sizes. Therefore, fluid flow becomes more favorable. The precipitation is not critical determinant of alteration process, despite the high proportion of small pores. For heterogeneous sample, both dissolution and precipitation significantly affect to alteration of pore structure. Particularly, the precipitation seriously damaged to the main flow channels. These undesirable effects on fluid flow appeared at injection point, which was exposed to fresh CO2 for a long time. This study suggests that pore structure analysis allows a more exact interpretation and judgment of the alteration of pore structure by dissolution and precipitation and can assist in designing injection plans, particularly near the injection area or in complex pore structure.