3D type flower-like ZnO nanostructure is fabricated on GaN epitaxial layer by hydrothermal synthesis. The formation of ZnO nanostructures is controlled dominantly by pH of the aqueous solution. The microstructure of flower-like ZnO nanostructure was examined by FE-SEM, XRD and FE-TEM. It is found that the shape of ZnO nanostructures are likely flower and chestnut bur shapes. FE-TEM and XRD analysis shows that ZnO nanostructures are single crystalline. Some discussion is made on the mechanism of ZnO growth in solutions with different pH.