We report on the growth of ZnO nanocrystals having a hexagonal, prismatic shape, sized 700 nm × 600 nm, on bare indium tin oxide (ITO) substrates. The growth is induced by a low ion flux and involves a low-temperature electrodeposition technique. Further, vertically aligned periodic nanocrystal (NC) growth is engineered at predefined positions on polymer-coated ITO substrates patterned with ordered pores. The vertical alignment of ZnO NCs along the c-axis is achieved via ion-by-ion nucleation-controlled growth for patterned pores of size ≈600 nm; however, many-coupled branched NCs with hexagonal shape are formed when a patterned pore size of ≈200 nm is used. X-ray diffraction data is in agreement with the observed morphology. A mechanism is proposed to interpret the observed site-specific oriented/branched growth that is correlated to the pore size. As ordered NC arrays have the potential to generate new collective properties different from single NCs, our first demonstration of a cost effective and facile fabrication process opens up new possibilities for devices with versatile functionalities.