This work summarizes the recent progress on the thermal transport properties of 3D nanostructures, with an emphasis on experimental results. Depending on the applications, different 3D nanostructures can be prepared or designed to either achieve a low thermal conductivity for thermal insulation or thermoelectric devices or a high thermal conductivity for thermal interface materials used in the continuing miniaturization of electronics. A broad range of 3D nanostructures are discussed, ranging from colloidal crystals/assemblies, array structures, holey structures, hierarchical structures, to 3D nanostructured fillers for metal matrix composites and polymer composites. Different factors that impact the thermal conductivity of these 3D structures are compared and analyzed. This work provides an overall understanding of the thermal transport properties of various 3D nanostructures, which will shed light on the thermal management at nanoscale.