Various annealing conditions (environment, temperature, and duration) are applied to study the nanoscale Kirkendall effect of copper (Cu) nanowire (NW) arrays on a Si substrate. The results show that an appropriate amount of oxygen supply is crucial for uniform transformation from Cu NWs (average diameter ∼50 nm) into Cu oxide nanotube arrays. An annealing duration of 30 min at 200 °C in a low vacuum environment reveals that the voids are not uniformly distributed at the Cu/Cu oxide interface. This suggests that void growth is due to surface diffusion of Cu along void surfaces. Annealing above 200 °C for 60 min resulted in complete transformation from Cu NWs into Cu oxide nanotubes. X-ray photoelectron spectroscopy characterization indicates that the Cu oxides formed at 200 °C and 300 °C are Cu2O and CuO, respectively. It is demonstrated that the transformation from Cu NW arrays into Cu oxide nanotube arrays can be combined with the joining of stacked Si chips in a single-process step with reasonable joint shear strength. Transmission electron microscopy-electron energy loss spectroscopy elemental mapping analysis reveals that the joint interface is Cu oxide. The outward diffusion of Cu driven by the nanoscale Kirkendall effect is believed to enhance the joining process. By controlling the environment, temperature, and duration, joined Cu2O or CuO nanotube stacked chips can be achieved, which serve as a platform for the further development of nanostructured, stacked devices.