Non-equilibrium molecular dynamics simulation was used to examine the effects of a nanostructure surface on thermal transport across solid-liquid interfaces, based on spectral analyses. We modelled five types of nanostructure (< 3.0 nm) at a solid-liquid interface, and investigated overall interfacial thermal resistance (ITR) with the corresponding spectral heat flux (SHF) across the structured solid-liquid interface. We also focused on local interfacial regions consisting of the structured surface, and quantitatively evaluated local ITR and SHF which are essential to understanding overall thermal transport mechanisms at a structured interface. The results of the overall SHF analysis across the structured interfaces showed that a nanostructure suppresses interfacial thermal transport at the relatively high frequency (~ 4 THz) which is dominant at a flat interface. The calculated local SHF showed characteristic profiles corresponding to the local regions of the structure; narrow interfacial regions showed heat flux spectra dominated by the relatively low frequency (~ 2 THz), which causes reduced local ITR. These results suggest that a nanostructure on a solid-liquid interface can modulate overall ITR changing spectra of the overall thermal transport across the interface, and that understanding local thermal transport across a structured surface in overall thermal transport is important to more precisely elucidate thermal transport mechanism across a structured solid-liquid interface.