A multiscale modeling method is put forward to investigate the interfacial characteristic of copper nano interface structures. The ISE (Interface Stress Element) method is set as a coupling button to a span-scale model combined with MD (Molecular Dynamics) and FE (Finite Element) methods. Those three methods are effectively coupled by MD-ISE and ISE-FE handshake regions. The thermal properties of copper nano structures are investigated by using this multiscale model. The results show that the accuracy of the MD-ISE-FE model is better than that of MD-FE model; the thermal resistance decreases with the temperature increase. Compared with the MD-FE model, the MD-ISE-FE multiscale model can provide better accuracy to investigate the interface prosperities for MEMS design and manufacturing. (C) 2014 Elsevier Ltd. All rights reserved.