Wave effects of phonons can give rise to controllability of heat conduction in nanostructures beyond that by particle scattering at surfaces and interfaces. In this paper, we propose a new class of three-dimensional nanostructures: a silicon-nanowire-cage (SiNWC) structure consisting of silicon nanowires (SiNWs) connected by nano-cross-junctions. We perform equilibrium molecular dynamics simulations and find an ultralow value of thermal conductivity of SiNWC, 0.173Wm−1 K−1,which is one order lower than that of SiNWs. By further modal analysis and atomistic Green’s function calculations, we identify that the large reduction is due to significant phonon localization induced by the phonon local resonance and hybridization at the junction part in a wide range of phonon modes. This localization effect does not require the cage to be periodic, unlike the phononic crystals, and can be realized in structures that are easier to synthesize, for instance in a form of randomly oriented SiNW network.