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In this paper, in order to effectively utilize salt lake magnesium resources, we focused on a functional material containing magnesium, i.e. magnesium oxide, MgO, which is a type of antibacterial material. Through a first-principles study from the atomic level, the microstructure of MgO containing doped point defects of different elements was studied. The relationship between the microscopic structure of the material and its special antibacterial function was explored. The results are as following: the interstitial impurities in MgO are more helpful than substituted impurities for the improvement of the electronic structure. The analysis of the influence of different doping elements on the microstructure confirmed theoretically that Ag and Cu have the same highly active antimicrobial properties with the same change of microstructure, thereby confirming the relationship between microstructure and antimicrobial activity. The results of the simulations match the experimental results, thereby theoretically demonstrating the relationship between defects and antibacterial activities and providing further insight into the nature of the antibacterial mechanism.