Objective To investigate the thermodynamic mechanisms of the intermetallic compound (IMC) formation and Sn whisker growth in Sn-Cu bilayer thin film system. Methods Using the interface thermodynamics theory, the IMC formation and the Sn whisker growth were studied through calculating the corresponding surface energies, interface energies and critical thickness. Results The IMC Cu6Sn5 was firstly formed at the triple junction of Sn grain boundary and Sn/ Cu interface and then grew along the Sn/ Cu interface. The resulting stress gradient drove the diffusion of Sn atoms to the surface and formed Sn whisker on it. Conclusion The Sn whisker growth was caused by the IMC formation in Sn sublayer, based on which some methods were proposed for inhibiting the growth of Sn whisker.