With the devices miniaturization, the properties of materials at the micro/nano scale were much different from what at Macro-scale because of the scale effect. The Interface Stress Element (ISE) was introduced into the multi-scale model. These three methods, Molecular Dynamics (MD), ISE and Finite Element (FE) were effectively combined by designing a handshake region and using the transition interface element method. The multi-scale model of film was built based on MD-ISE-FE. The sequential coupling method was used to calculate, and then, the results of the FE and ISE region were applied to the MD region. The EAM potential was used to simulate. The results were the basically same with the other experimental and simulation results in the reference. It indicated that the multi-scale analysis method could be applied to calculate the thermodynamics properties of the interface structure at the Micro/nano scale.