Ultrasonic welding (UW) is an important joining technique in the electrical industry. Molecular dynamic simulation has been shown to possess several advantages for revealing the evolution of the atomic-scale structure and the interpretation of diffusion mechanisms at the microscopic level. However, voids associated with the understanding of microstructure evolution in the weld zone and dynamic processes that occur during ultrasonically welded materials still exist, and no UW studies at the atomic scale have so far been reported. In this study, molecular dynamic simulations of UW between Al and Cu were performed to investigate the diffusion behaviors of Al and Cu atoms. The results confirmed the occurrence of asymmetrical diffusion at the Al/Cu interface during UW. Meanwhile, recovery was noticed in the disordered Al blocks at low temperature. The thickness of the diffusion layer increased with the welding time. For relatively long welding times (1 ns), the concentrations of Al and Cu revealed the appearance of phase transitions. In addition, the diffusion during UW was identified as a dynamic and unsteady process. The diffusion coefficient was much larger than that underwent during the steady diffusion process despite the low interfacial temperature (below 375 K), which was mainly attributed to shear plastic deformation at the interface.