In the present work, the nanoindentation of aluminum thin film on silicon substrate is investigated by three-dimensional molecular dynamic (MD) simulation. The film/substrate system is modeled by taking Lennard-Jones (LJ) potential to describe the interaction at the film-substrate interface. Different loading rate from 50 to 250 m/s is carried out in the simulation. The results showed that the hardness of the film increased with the loading rate. In order to study the effect of substrate on the mechanical properties of thin film, nanoindentation process on monolithic Al material is also simulated. The simulation results revealed that indentation pile-up in the aluminum film is significantly enhanced by the substrate. The substrate also affects the loading force during the nanoindentation. At the beginning of the indentation, the loading force is not affected by the substrate. Then, it is getting smaller caused by the interface. As the film is penetrated, the loading force increased rapidly caused by the hard substrate. These results were coincident with the previous reported experiments. Crown Copyright (C) 2010 Published by Elsevier B. V. All rights reserved.