Experiments and atomistic simulations have suggested the existence of a direct correlation between the wetting properties of a surface and heat transfer across it. In this investigation, molecular dynamics simulations of surface wettability and solid–liquid thermal transport were conducted in order to better understand the relationship between the surface chemistry and thermal transport. The wettability transparency of graphene-coated surfaces was considered in order to investigate heat transfer across a complex interface with similar wettability as a bare surface. The results indicate that the relationship between the interfacial heat transfer and wettability is not universal. The density depletion length was found to reconcile the thermal boundary conductance calculations for different bare and graphene-coated silicon surfaces.