A significant issue for GaN-based high-electron-mobility transistors (HEMTs) in high power devices is the material defect, particularly the defect states generated by the defects, which has a negative impact on the device carrier concentration and carrier transport. Based on density functional theory (DFT), we investigate the microscopic properties of different type point vacancies in the AlGaN/GaN heterojunction. It is found that N vacancy introduces defect states near the conduction band minimum (CBM) of the GaN layer and AlGaN/GaN interface. Ga and Al vacancies introduce defect states near the valence band maximum (VBM) in bulk and interface of AlGaN/GaN heterojunction. Moreover, Al vacancy is more likely to be an effective candidate for acceptor defect than Ga vacancy. We further study several AlGaN/GaN interface passivation schemes by introducing F, V group element P, and III group element B at the AlGaN/GaN heterojunction interface to analyze the passivation mechanism. According to the results of the passivation models, B passivation of Ga and Al vacancies is an effective method to completely remove the defect states from Ga and Al vacancy defects. Combining the III and V groups elements into the passivated process may be effective in achieving high-quality AlGaN/GaN heterojunction interface for the future GaN-based HEMTs fabrication.