In this work, the structural defects and the thermal conductivity of CuO, ZnO, and CuO/ZnO nanowires have been studied, using molecular dynamics simulation with COMB3 potential. The initial parameters and atoms positions were taken from reports of bulk materials with tenorite and wurtzite structures, respectively. Nanowires were grown along the c-axis, as observed experimentally. The results confirm the defects apparition in the systems after simulation with a formation of grains to reduce the energy of the nanowires. In the CuO nanowires case, the lack of periodicity in the basal plane causes a contraction effect over the network parameter b of the monoclinic structure with a Cu-O distance reduction. [A constriction effect on inclined planes, as a product of surface charges, deforms the nanowire, generating undulations. In ZnO nanowires, a decrease in the Zn-Zn distance produced a contraction in the nanowire length. A constriction effect was evident on the surface charges. It presented a bond reduction effect, which was larger at the ends of the nanowire. In CuO/ZnO nanowires, the structural defects come from the distortions of the crystalline lattice of the ZnO rather than CuO. The thermal conductivity of the nanowires was calculated at temperatures between 200 K and 600 K using the Green–Kubo equation. Results showed similar values to those reported experimentally, and the characteristic maximum with similar trends to those observed in semiconductors. Our results suggest that structural defects appear in nanowires grown on the free substrate, and are not related to the lattice mismatch.