Geologic carbon sequestration (GCS) represents a promising approach to achieve global net-zero carbon targets. Kaolinite, a common component in natural sediments, plays critical roles as a caprock in GCS projects. Herein, molecular dynamics simulations are employed to investigate CO2 behaviors at the kaolinite-water interface, focusing on natural defects such as nanovalleys. Our findings reveal that the diffusion behavior of CO2 molecules varies depending on their proximity to different kaolinite surfaces. Specifically, CO2 near the hydrophobic siloxane surface, which exhibits a stronger affinity for CO2, demonstrates lower diffusion coefficients compared with molecules near the hydrophilic gibbsite and edge surfaces. This reduced mobility leads to prolonged residence times at the siloxane surface. Additionally, edge sites exhibit greater CO2 retention than gibbsite surfaces, likely due to their higher surface roughness and reactivity. Furthermore, our results indicate that CO2 primarily penetrates the nanovalley through the central region and areas adjacent to the siloxane surface. At elevated CO2 concentrations, nanobubbles begin to form; however, these nanobubbles are unable to enter the nanovalleys due to the presence of substantial breakthrough pressure barriers. This study enhances our understanding of CO2 behaviors in clay-rich environments and its application within the scope of sustainable chemistry related to the carbon neutrality strategy.