Using the atomic force microscopy, we have studied the effect of sputtering particle energy on the growth and microstructures of Mo thin films prepared on borosilicate glass (BK7) substrates with ion beam sputtering technique. With specially designed fixture, all samples were prepared in the same run, which diminished the effect of multi-runs on the growth of thin films. Furthermore,the morphology of Mo thin films was studied quantitatively based on numerical analy sis. The morphology of Mo thin films is typically fractal, and the surface para meters of thin films such as fractal dimensions, lateral correlation length and interface width are all obtained. Compared with the thin films prepared under the screen grid voltages of 300 and 700V, the interface width and lateral correlation length of the thin films prepared under the screen grid voltage of 500 V show two times large difference. All the fractal dimensions of thin films are n ear 2 and the growth process of Mo thin films can be described using Mullins diffus ion model. Besides, by using the technique of Auger electron spectroscopy, the atomic concentrations can be obtained in the depth profile.