Abstract: This paper simulated the effects of deposition energy and deposition rate on the morphology of three-dimensional thin films. The substrate is anisotropic periodic square-lattice. Atomic deposition,diffusion of re-evaporation was considered. Influences of the nearest neighbor and the next nearest neighbor were taken in to consideration when counting the barrier energy. The results showed that the deposition energy has significant influence on film roughness,substrate fill ratio and islands number. The deposition rate influenced the film roughness slightly. And it has a slender effect on the substrate fill ratio under the condition of low deposition energy,but when the deposition energy is high,the effect became significant. On conditions of high deposition energy and high deposition rate,in order to improve the film quality,and ensure the efficiency of film forming,properly decrease the deposition rate is more effective than properly reduce the deposition energy.