We report a facile and effective strategy for synthesizing morphology-controlled patterned ZnO nanostructures. Polymeric nanowell arrays were employed as scaffold templates, followed by solution dipping and calcination process, polygonal ZnO nanobowl structures were fabricated on silicon substrate. The ordered polymeric nanowell arrays not only provided confined areas for depositing desired materials, but also induced shape transition of ZnO nanobowls from circular to polygonal. The morphology of the patterned ZnO nanostructures can be easily controlled by tuning parameters of polymeric nanowell arrays and other treatment conditions. The patterned structures were characterized by field emission scanning electron microscopy (SEM), atomic force microscopy (AFM), X-ray diffraction (XRD) and thermogravimetric analysis (TGA).