We have developed an efficient scalable kernel method for thermal transport in open systems, with which we have computed the thermal conductance of a junction between bulk silicon and silicon nanowires with diameter up to 10 nm. We have devised scaling laws for transmission and reflection spectra, which allow us to predict the thermal resistance of bulk-nanowire interfaces with larger cross sections than those achievable with atomistic simulations. Our results indicate the characteristic size beyond which atomistic systems can be treated accurately by mesoscopic theories.