A novel method was proposed to fabricate a ZnO seed layer with a protrusion and matrix structure, and then ZnO nanorods could be synthesized on it using the hydrothermal method to form ZnO nanoflower arrays (NFAs) easily. A patterned sapphire with a matrix cavity was used as the template, ZnO gel was deposited on the multilayer substrates using spinning coating, and the prepared seed layer with a protrusion and an array-patterned structure was moved to a Si substrate using the lift-off method. Because the ZnO seed layer exhibited a matrix and protrusion structure, ZnO nanorods were grown vertically downwards and formed ZnO NFAs. The XRD patterns resulting from analyses showed that the diffraction peaks of the five growth directions of ZnO NFAs increased as growth time increased. Furthermore, SEM and FIB analyses indicated that the length, width, aspect ratio, and total surface area of ZnO NFAs grown on the transferred seed layer increased as the synthesis time increased. Different ZnO NFAs synthesized for varying synthesis times were used to investigate methylene blue degradation, with the effect of ZnO NFAs on methylene blue degradation determined using the Beer–Lambert law. Our results demonstrate that the effect of ZnO NFAs on methylene blue degradation was enhanced with increasing synthesis time.