A series of Ge quantum dot samples with different Ge thickness is grown on n-Si(100) substrates by ion beam sputtering. Their morphology and structure are characterizated using AFM and Raman spectra, in which the evolution of the morphology, density, dimension, crystalline, and composition of the Ge quantum dots are discussed in detail. The results show that after the growth mode transiting from 2-D to 3-D, the shape of the Ge quantum dot changes directly into a dome shape and no pyramid dots are observed. Besides, with the increase of the Ge deposition, the density of the quantum dots increases to a maximum and then decreases, the crystalline becomes better, but the Ge/Si alloying processing is enhanced and the Ge composition decreases in quantum dots at the same time.