Periodically distributed ZnO nanostructure arrays were hydrothermally grown on silicon substrates. For the preferential, site-selective growth of the ZnO nanostructures, a seed layer was patterned using self-assembled monolayers of polystyrene spheres (PSs) lithography technique. The size of the seed layer was controlled by the size of PSs, which was determined by oxygen plasma etching time. Due to the existence of numerous nucleation sites, flower-like (FL) ZnO nanostructures grew on the large seed layer over 800 nm in diameter. By reducing the size of the seed layer, we could make a couple of ZnO nanowires grow on a single seed layer island. We examined the cathodoluminescence (CL) spectra of FL ZnO nanostructure arrays and coupled (CO) ZnO nanowire arrays. Since the dimension of the nanostructures is smaller than or comparable to the penetration depth of the incident electron, CL signal would be generated in the whole body of the nanostructures. So, the CL intensity might be proportional to the surface area through which the photons could escape. As a result, it is natural that the CL intensity from the FL ZnO nanostructure arrays should be stronger than that from the CO ZnO nanowire arrays. However, in spite of the smaller surface area, the CL intensity was strikingly enhanced in the CO ZnO nanowire arrays compared with the closely-packed ZnO nanowire arrays. It could be attributed to the suppression of the near-band-edge ultraviolet emission in the [0001] direction, which was observed in the monochromatic CL measurement.