In 3D integration package using TSV technology, bonding is the core technology for stacking and interconnecting the chips or wafers. During bonding process, however, warpage and high stress are introduced, and will lead to the misalignment problem between two chips being bonded and failure of the chips. In this paper, a finite element approach is used to predict the warpages and stresses during the bonding process. In particular, in-plane deformation which directly affects the bonding misalignment is closely analyzed. Three types of bonding technology, which are Sn-Ag solder bonding, Cu-Cu direct bonding and SiO2 direct bonding, are compared. Numerical analysis indicates that warpage and stress are accumulated and become larger for each bonding step. In-plane deformation is much larger than out-of-plane deformation during bonding process. Cu-Cu bonding shows the largest warpage, while SiO2 direct bonding shows the smallest warpage. For stress, Sn-Ag solder bonding shows the largest stress, while Cu-Cu bonding shows the smallest. The stress is mainly concentrated at the interface between the via hole and silicon chip or via hole and bonding area. Misalignment induced during Cu-Cu and Sn-Ag solder bonding is equal to or larger than the size of via diameter, therefore should be reduced by lowering bonding temperature and proper selection of package materials.