In the present study, we focused on the atomic−scale structures: step, vacancy, cluster, and adatom at a solid−liquid interface, and investigated effects of the structures on the thermal transport across the interface to elucidate fundamental thermal transport mechanism at the atomic scale. The study was based on the molecular dynamics analysis, and the thermal transport property was examined comprehensively by spectral analyses. The detailed results showed that the atomic−scale structures can decrease the thermal boundary resistance of the solid−liquid interface, and the structure of the adatom enhances the thermal transport across the interface the most. It's also found that the thermal transport is enhanced by the change of the vibrational states of the surface solid atoms constituting the edge region of each structure, which was also confirmed by the analyses using the spectral heat fluxes across the interface. Furthermore, the thermal energy transport through the atomic−scale structures is enhanced by the modes vertical to the macroscopic heat flux direction, which is a key factor for modulating the thermal transport at the atomic scale.