Moss biocrusts are the critical active cover on the surface, with various ecological functions such as improving soil properties, fixing soil and water, sequestration of carbon and nitrogen, and microbiological community is the main component of Moss biocrusts to play its ecological function. To explore the wet area of lithophytic moss biocrusts microbial community composition and diversity characteristics, reveal its development and functional mechanism, our study focused on the lithophytic moss biocrust in five sampling sites of Niyu, Cheyu and Luoyu at the northern foot of the Qinling Mountains, used high throughput sequencing technology, analyzed the lithophytic moss biocrusts microbial community composition, abundance, diversity, and determined the relationship between nutrients and microbial community, to provide theoretical basis for the ecological restoration of bare rock wounds. The results show that: (1) the total nitrogen and organic matter contents of Qinling lithophytic moss biocrusts are between 4.16 to 8.26 g/kg and 89.44 to 131.05 g/kg, respectively, and the differences between the sampling site are significant; whole phosphorus and potassium was low, ranging from 0.88 to 1.21 g/kg and 13.50 to 18.10 g/kg, respectively. (2) Bacteria in the Qinling lithophytic moss biocrusts account for more than 80% of the microbial community, and the diversity of bacteria is much higher than that of fungi; Among them, the predominant bacterial flora are Proteobateria, Bateroidetes, Actinobacteria and Acidobacteria, and the dominant community of fungi are Ascomycota and Mortierellomycota. (3) The Redundancy analysis (RDA) shows that total potassium and organic matter significantly impact the structure of the predominant bacterial community. Proteobacteria and Bacteroidetes are suitable for living in the soil with high humidity and good nutrition; whole phosphorus and organic matter significantly influence the structure of the predominant fungal community, and the Mortierellomycota has more growth advantage in low phosphorus soil. It is found that bacteria are the main microbe of Qinling lithophytic moss biocrusts. Compared with the native situation in the arid region, Qinling lithophytic moss biocrusts showed significantly lower content of the Actinobacteria and Acidobacteria; for fungi, the relative abundance of Ascomycota and Basidiomycetes has significantly decreased, and significantly higher of Mortierellomycota. Organic matter is the most important nutrient factor affecting the composition of the microbial community in the moss biocrusts. The rich nutrients make the microbial community structure of lithophytic moss biocrusts in wet areas more complex and diverse and showed higher abundant species composition.