[Objective] In order to understand the microbial community structure and microbial diversity which was obtained at nine soil samples (primary, secondary saline alkali soil and farmland soil) in saline alkali soil from the area of Hexi Corridor. [Methods] Soil microbial total DNA was extracted. The microbial community structure and diversity were analyzed by using Illumina Miseq high-throughput sequencing system. [Results] Total of 325 089 partial 16S rRNA gene sequences were obtained from the samples. Redundancy analysis and heatmap analysis showed that the microbial community composition were quite different between primary and secondary saline alkali soil, and were different between primary saline alkali soil and farmland soil, but the composition of secondary saline alkali soil and farmland soil were similar. Soil pH effected on microbial community composition was the most significant. The diversity index and rarefaction curves analysis showed that in nine soil samples, the lowest microbial diversity was No. 1 sample from primary saline alkali soil and the highest microbial diversity was No. 6 sample from secondary saline alkali soil. Saline alkali soil mainly comprised nine phyla, among which Proteobacteria was the dominant population, followed by Actinobacteria, Bacteroidetes, Acidobacteria, Planctomycetes, Chloroflexi, Gemmatimonadetes, Firmicutes and Verrucomicrobia. Proteobacteria was the dominant population in primary saline alkali soil and farmland soil. Acidobacteria was the dominant population in secondary saline alkali soil. [Conclusion] Microbial diversity in the Hexi Corridor saline alkali soil was very rich, there were a large quantity of microbial groups, especially in the secondary saline alkali soil.