In order to investigate the Atomic Force Microscope(AFM) based nanoindentation process of monocrystalline copper film,a three-dimensional molecular dynamic simulation model of nanoindentation process was established.The Morse potential was used to compute both the effect of interactions between the specimen atoms,and between specimen atoms and indenter atoms.Nanoindentation processes were conducted to evaluate the indentation depths (0,0.361,0.722,1.083 nm) on the indenter stress and variations of system potential energies.The results show that the plastic deformation via amorphous transformation is caused by the mechanism of nanoindentation of monocrystalline copper film.With the increase of indentation depth,both of the variations of system potential energies (range of -83 900～-83 400 eV at the maximum indentation depth) and the force (range of -0.3～70 nN at the maximum indentation depth) increase,which shows a strong size effect.