The synthesis of ZnO nanostructures via the transformation strategy from zinc-based compounds has long been hampered by the difficulties in obtaining high quality nanostructures. Herein we report a simple and effective method toward nanocrystalline/nanoporous ZnO nanostructures with well-defined shapes transformed from zinc fluorohydroxide Zn(OH)F deposited on Si substrate. The traditional reaction route of zinc chloride-hexamethylenetetramine system toward ZnO was deviated by the use of fluorion (F⁻) additive through a simple solvothermal process in H₂O–ethanol component solvent, resulting in the formation of Zn(OH)F crystals. Three kinds of micron shape (sphere, hexapod and hexagonal disk) and two kinds of microstructure (nanocrystalline and nanoporous) were demonstrated, merely by varying the concentration of F⁻ ions and the sintering temperature. While the concentration of F⁻ ions directly determined the phase and morphology of the as-deposited nanostructures, the ultra smooth nature of the Si substrate and the component solvent affected significantly the nucleation, the self-assembly behavior and the crystallinity of each Zn(OH)F prism. The formation mechanism of Zn(OH)F hexapod was discussed from two points, the Si-controlled nucleation on already-formed particles, and the [F⁻]-dependent crystallization process. Furthermore, the self-assembly of multiple Zn(OH)F/ZnO disks and the selective growth of Zn(OH)F hexapods was demonstrated by reducing the growth rate and by inducing the nucleation on the patterned gold layer, respectively.