In this paper, the self-assembly technology is investigated in order to apply on the alignment method to achieve rapid and accurate multichip-to-wafer stacking. By virtue of distinct liquid surface tensions between hydrophilic and hydrophobic materials, the hydrophilic chips can be self-aligned to the hydrophilic substrate which is defined by the surrounding hydrophobic substrate. The surface quality of hydrophobic film with self-assembled monolayers (SAMs) based on self-assembled mechanism strongly affects the performance of alignment. The surface quality of SAMs film which depends on experimental parameters such as dip-coating time and heating time is critical to determine the accuracy of alignment. Moreover, the chip shape and size also have an impact on the alignment accuracy. By improving the misalignment, a good design by the self-assembled mechanism for the self-alignment method can be applied in the bonding technology.