Abstract:[Background] In open-pit coal mining in arid areas, the dust is destined to aggravate soil environment deterioration and air quality decline. A few studies on the microbial community structure in soil and dust particles in coal districts are available. [Objective] To study the microbial community structure and diversity of soil, dust, and atmospheric PM2.5 from different functional regions in the open-pit coal mine in Nanhu Township, Hami, Xinjiang. [Methods] Illumina NovaSeq was employed for high-throughput sequencing to characterize the community structure and functional diversity of bacteria and fungi in the three media in the open pit area and fly ash area. [Results] Ascomycota and Basidiomycota dominated the fungi, while Proteobacteria and Actinobacteria were the dominant bacterial phyla in the coal district. The abundance and diversity of fungal and bacterial communities showed no significant difference in the entire coal district, but the niche breadth of bacterial communities in atmospheric PM2.5 was significantly larger than that in the open pit area and the fly ash area. Some functional groups with significant difference in abundance were found between soil and atmospheric PM2.5 in the coal district, such as saprophytic trophic fungi, methanotrophic bacteria, and chitinase-producing bacteria. [Conclusion] The dust produced in open-pit coal mining has important impact on the microbial community structure in soil and atmospheric PM2.5 in the coal district. The specific coal components-degrading microbes are among the main contributors to the soil ecological safety in mining area.