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With the development of micro/nanoelectronic technology and the miniaturization of IC (Integrated Circuit) packaging, the interfacial characteristics of the nanoscale interface structure in IC packaging become more and more serious on the whole performance of IC or devices. The FEM (finite element method) is used to estimate the thermodynamics properties of the Al-Cu interface structures at the macroscopic scale. Meanwhile, the NEMD (non-equilibrium molecular dynamics) method is used to investigate the interfacial heat transfer at the nanoscale. In the macroscopic scale, the deformation and nanocracks always appear at the outside edge of interface between Cu solder and Al pad due to the dissimilar thermal expand expansion coefficients. In the nanoscale, there is diffusion between different atoms at the interface, the diffusion thickness increases with the temperature increasing. The diffusion between Al and Cu atoms enhances the heat transfer with the temperature increasing. The results reveal the mechanism of the interfacial heat transfer and interfacial crack, which also supply a multiscale analysis method to evaluate the interfacial properties in the IC packaging, which is helpful to design and manufacture of IC assembly.