Si（001） chips were implanted by Zn ions of 40 keV with different ion dosages and are annealed in air at different temperatures. Atomic force microcopy， transmission electron microcopy， X-ray diffraction and electron probe are applied to study the microstructure， morphology and chemical composition of the chips, either as-implanted or annealed at different temperatures. It was found that the as-implanted Zn atoms aggregate into clusters scattering about 35 nm beneath the surface of the chips. During the annealing process， Zn atoms are found to migrate towards the surface of the chips and aggregate into nanoparticles at the interface between the amorphous SiO2 layer and polycrystal line Si layer. Annealing temperature was found to be the crucial factor controlling the formation of ZnO nanoparticles. ZnO nanoparticles begin to appear at about 400 ℃ and the diffraction intensity of ZnO becomes strong while the diffraction intensity of metallic Zn weakens with increasing annealing temperature. At the annealing temperature of 800 ℃， Zn2SiO4 phase was observed due to the reaction between ZnO and SiO2 or Si.