In this study, we perform molecular dynamics simulations to investigate the desublimation of carbon dioxide (CO₂) on hydrophilic and hydrophobic surfaces with nanostructures. The results reveal that the presence of surface nanostructures substantially reduces the temperature threshold for CO₂ desublimation relative to that observed on smooth surfaces. On hydrophilic surfaces, the adsorption layer is found to be considerably thicker, and the surface topography disrupts the spatial ordering of CO₂ molecules at the liquid–solid interface, delaying nucleation onset by 65.68% relative to the smooth surface in the representative trajectory. In contrast, the introduction of nanostructures effectively increases the heat transfer area on hydrophobic surfaces, thereby promoting CO₂ condensation and accelerating the overall desublimation process, with a 42.86% reduction in nucleation onset time on structured surfaces. These findings suggest that the judicious selection of surface wettability and morphology enables tunable control over both condensation and nucleation kinetics, which holds practical implications for the design of efficient carbon capture systems.