Assemblies of metal oxide nanowires in 3D stacks can enable the realization of nanodevices with tailored conductivity, porous structure and a high surface area. Current fabrication methods require complicated multistep procedures that involve the initial preparation of nanowires followed by manual assembly or transfer printing, and thus lack synthesis flexibility and controllability. Here we report a general synthetic orthogonal assembly approach to controllably construct 3D multilayer-crossed metal oxide nanowire arrays. Taking tungsten oxide semiconducting nanowires as an example, we show the spontaneous orthogonal packing of composite nanorods of poly(ethylene oxide)-block-polystyrene and silicotungstic acid; the following calcination gives rise to 3D cross-stacked nanowire arrays of Si-doped metastable ε-phase WO3. This nanowire stack framework was also tested as a gas detector for the selective sensing of acetone. By using other polyoxometallates, this fabrication method for woodpile-like 3D nanostructures can also be generalized to different doped metal oxide nanowires, which provides a way to manipulate their physical properties for various applications.