Objective: To study the levels of atmospheric PAHs in Nanjing, and explore the correlation between PAHs and air microbial community. Methods: The concentration of atmospheric PAHs was determined by GC-MS, and microbial community diversity was analyzed by 16S rRNA gene sequencing. Pearson correlation analysis was conducted between the concentration of atmospheric PAHs and the microbial community. Results: It was found that Phe, Fla and Pyr are the main components of atmospheric PAHs. The total concentration of atmospheric PAHs in 2019 was higher than that in 2020. The concentration of atmospheric PAHs in autumn of 2019 was significantly higher than that in spring. At the level of phylum, the dominant phylum in both 2019 and 2020 are Firmicutes, Actinobacteria and Proteobacteria. In terms of genus, Bacillus is the common dominant bacteria of 2019 and 2020. In the correlation analysis between PAHs and microbial populations, it was found that the abundance of Bacillus in Firmicutes and Micrococcus in Actinobacteria were correlated with atmospheric PAHs. Conclusion: Atmospheric PAHs pollution may be related to the changes of species and abundance of air microorganisms which may be potential health risks.