Caprocks play a crucial role in geological storage of CO2 by preventing the escape of CO2 and thus trapping CO2 into underlying porous reservoirs. An evaluation of interaction-induced alteration of hydromechanical properties of caprocks are essential to better assess the leaking risk and injection-induced rock instability, and thus ensuring a long-term viability of geological CO2 storage. We study the changes in nanopores, elastic velocities and mechanical responses of a carbonate caprock due to rock-water/brine-CO2 interaction (CO2 pressure ~ 12 MPa; 50 ?). Before the interaction, the total and accessible porosities are 1.6% and 0.6%, respectively, as characterized by the Small Angle Neutron Scattering (SANS) technique. SANS results show that the total porosity of the carbonate caprock increases apparently due to rock-brine-CO2 interaction and the increasing rate rises as brine concentration increases (2.2% for 0M NaCl, 2.6% for 1M NaCl, and 2.7% for 4M NaCl). The increase total porosity is due to the dissolution of calcite which tends to enlarge accessible pores (by 0.8%-1.2%) while slightly decrease the inaccessible pores (by 0.1%-0.2%). Under CO2-acidified water environment, P- and S-wave velocities (5536.7 m/s and 2699.7 m/s) of a core sample containing natural fractures decreases by 8.5% and 8.1% respectively, while both P- and S-wave velocities (6074.1 m/ s and 3858.8 m/s) for a intact sample show only ~0.5% decreases. The interaction also causes more than 50% degradation of the uniaxial compressive strength for the core sample with natural fractures. We also conduct simulations of the single-phase creeping flow and two-phase water-CO2 flow in micron-scale natural fractures, as extracted from X-ray Micro-CT images of the core sample. The simulated absolute permeability (2.0×10-12 m2) is much higher than the matrix permeability (6.7×10-20 m2before the interaction; 1.3×10-19 m2after the interaction), as calculated based on the Kozeny-Carman Equation. This indicates that natural fractures provide preferential flow paths for CO2 while flow through caprock matrix can be reasonably neglected. Simulation results also indicate that CO2 preferentially migrates in the natural fractures where there are more inter-connected and permeable channels. The study recommends that more attention should be addressed on interaction-induced alteration of fracture/faults permeability/stability, and its effect on the sealing integrity of carbonate caprocks.