Abstract: Considering the phenomena that the position of basal atoms range from high and low or are unordered and its cause of the influence of inhomogeneous interaction energy between basal atoms and adsorbed atoms on the growth of the second layer atoms of 3D thin film,this paper established a early growth model of 3D thin film to study the influence of deposition rate,deposition energy,discrete degree and distribution form of inhomogeneous interaction energy on the early growth of 3D thin film on FCC（100） substrate. Due to the inhomogeneous distribution of substrate,this paper fits it for a certain range of random distribution. The simulation results show that inhomogeneous interaction energy have a significant influence on the early growth of 3D thin film under moderate temperature（T = 450K）; Reducing discrete degree and increasing concave and convex degree of distribution form for inhomogeneous interaction energy appropriately has a great influence on the early growth mechanism and island number of thin film.