We have studied the thermal conductivity of Ge and Si allotrope heterostructured nanowires (NWs) synthesized by phase transformation. The NWs are composed of successive hexagonal 2H and cubic diamond 3C crystal phases along the 〈111〉 axis. Using 3ω-scanning thermal microscopy on NWs embedded in a silica matrix, we present the first experimental evidence of thermal conductivity reduction in such allotrope 2H/3C heterostructured NWs. In Ge heterostructured 2H/3C NWs, similarly to homogeneous 3C NWs, we show a thermal conductivity reduction when the NW diameter decreases. In addition, in Si and Ge NWs, we observe a reduced thermal conductivity due to the heterostructuration 2H/3C. We evidence that the temperature of phase transformation, which influences the size and the number of 2H domains, can constitute an efficient parameter to tune the thermal conductivity.