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Thermosonic flip chip (TSFC) bonding is a developing area in array microelectronic interconnection technology, and ultrasonic vibration plays an important role in TSFC bonding. To understand the ultrasonic effects at the bonding interface, a lab bonder is constructed, TSFC bonding is realized, and some ultrasonic effects (plastic deformation of the bumps on the bond pads, atom diffusion, and increased dislocation density) are observed. A dynamic finite element model of TSFC bonding is developed to analyze the stress and strain distribution at the bonding interface. The results of our study show that ultrasonic vibration causes a large cycled stress of about 288 MPa at the bonding interface, which: 1) increases dislocation density, forms dislocation nets, and provides fast diffusion channels, and 2) increases the stress gradient, provides the driver force for atom diffusion, and increases the atom diffusion flux. The large cycled stress plays a key role in forming a 25-nm diffusion layer and a good bonding strength in 100 ms at the TSFC bonding interface.