Ordered ZnO nanorod arrays were epitaxially grown on GaN substrates by a hydrothermal method. The patterned template was made by transferring a self-assembled close-packed monolayer of polystyrene ( PS ) nanospheres onto GaN substrates. Then magnetron sputtering of SiO2 was used to mediate the size of PS nanospheres by plasma etching and form periodic seed sites for the following ZnO growth. It was observed that the size of ZnO nanorods could be varied by changing the temperature of hydrothermal growth, and the relationship between height and diameter of nanorods versus growth temperature was studied. This work provides a potential low-cost hydrothermal method for the preparation of ordered semiconductor nanorod arrays.