Objective The survival and adaptation mechanisms of microorganisms in desert soils and their ecosystem functions are of great significance for revealing the process of material transformation in arid areas.Method In this study, 16 transects were set up along the gradient of natural precipitation from the southeast to northwest of the Hexi Corridor. High-throughput sequencing technology was used to explore the characteristics of soil bacterial and fungal community diversity, revealing microbial diversity, dominant flora and soil mechanical composition, and nutrients relationship.Result The results showed that Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant communities in the desert soil bacteria of the Hexi Corridor. The abundance of Firmicutes is up to 85%. Ascomycota and Basidiomycota are the dominant fungi communities, and their relative abundances are both greater than > 5%. Correlation analysis showed that: coarse powder particles (0.05-0.02 mm), fine powder particles (0.25-0.10 mm), clay particles (< 0.002 mm), available phosphorus(AP)and alkalization nitrogen (AN) have a great influence on bacterial diversity Significantly, fine powder (0.25-0.10 mm), clay (< 0.002 mm), available phosphorus (AP) and alkalization nitrogen (AN) have a significant impact on fungal diversity (P < 0.01). Redundant analysis showed that fine powder (0.25-0.10 mm), available phosphorus (AP) and soil organic carbon (SOC) had significant effects on bacterial communities, while clay particles (< 0.002mm) and available phosphorus (AP) had significant effects on fungal communities (P < 0.05).Conclusion The results of this study explored the composition, changes and influencing factors of the desert soil microbial community structure in the Hexi Corridor, explained the influence of the soil environment on the distribution of microbes and the role of microbes on the development of the soil ecosystem, and served to protect biodiversity and desert ecosystem Provide theoretical reference.