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The aim of this article was to provide a systematic method to perform molecular dynamics simulation or evaluation for nano-scale interfacial friction behavior between two kinds of materials in MEMS design. Friction is an important factor affecting the performance and reliability of MEMS. The model of the nano-scale interfacial friction behavior between two kinds of materials was presented based on the Newton’s equations of motion. The Morse potential function was selected for the model. The improved Verlet algorithm was employed to resolve the model, the atom trajectories and the law of the interfacial friction behavior. Comparisons with experimental data in other paper confirm the validity of the model. Using the model it is possible to simulate or evaluate the importance of different factors for designing of the nano-scale interfacial friction behavior between two kinds of materials in MEMS.