According to orthogonal experimental design, a series of thin germanium films were grown by ion beam sputtering, then annealed. These films were characterized using AFM images. It was observed that the surface morphology of germanium films varied at different conditions. When the Ge film of 2.8 nm thickness was annealed at 600°C for 10 min, Ge islands appeared with a lateral size of about 50 nm and a height of about 4 nm. When the Ge film of 10 nm thickness was annealed at 720°C for 120 min, the amount of Ge islands increased and distributed uniform. Finally, the mechanism of ion beam sputtering and the diffusion between Si and Ge atoms were used to explain the results of morphology variation.