SnO₂(ZnO:Sn)_m is a recently reported new phase in the ZnO–SnO₂ binary system with a naturally grown superlattice structure, which is currently only found in the form of one-dimensional nanowires. Difficulties in high-purity synthesis and orientation control have hindered further investigations into its potential unique physical properties. Here, we present a novel growth design of fabricating ZnO/SnO₂(ZnO:Sn)_m binary/superlattice heterojunction nanowire arrays by one-batch chemical vapor deposition to explore the rational growth mechanism of SnO₂(ZnO:Sn)_m superlattice nanostructures. The morphology, chemical composition and crystal structure of the as-prepared products were characterized by scanning electron microscopy, X-ray diffraction, energy-dispersive spectroscopy, X-ray photoelectron spectroscopy and Cs-corrected scanning transmission electron microscopy. It is revealed that the SnO₂(ZnO:Sn)_m superlattice section epitaxially grows on top of the ZnO nanowire along the [0001] direction, following the orientation relationships [10]_Au//[110]_{ZnO/SnO2(ZnO:Sn)m} and (111)_Au//(0002)_{ZnO/SnO2(ZnO:Sn)m}. The Au catalysts on the pre-grown ZnO nanowires play a key role in absorbing further loading of Zn/Sn vapor, inducing the formation of the SnO₂(ZnO:Sn)_m superlattice on the basal plane of ZnO, at the same time, avoiding the appearance of Sn-rich impurity phases. Photoluminescence measurements display a red shift of the ultraviolet (UV) emission peak from 381 nm to 386 nm and an extra peak at 470 nm, compared with the ZnO reference. This study would shed light on the rational growth of natural oxide superlattice nanowire arrays and complex axial heterojunction nanostructures.