The goal of this study was to research the cyanobacterial diversity and distribution in algal crusts of Gurbantunggut Desert by the clone library method. In this paper, 10 representative algal crust soil samples were collected in different regions of the Gurbantunggut Desert, and the cyanobacterial 16S rRNA and psbA gene clone libraries were constructed and performed phylogenetic analysis. Moreover, the correlation of cyanobacterial diversity and abundance with environmental factors was analyzed to acquire the distribution characteristics and influencing factors of cyanobacteria. The results showed: (1) the cyanobacterial 16S rRNA gene belonged to 10 genera of 6 families (accounted for 94.85% of the total library) and an uncultured cyanobacteria by phylogenetic analysis. Oscillatoria and Microcoleus accounted for 42.54% and 37.16% of the library respectively, which were the dominant genus of cyanobacteria in Gurbantunggut desert. Only 4 genera of 4 families cyanobacteria were identified with the psbA gene by phylogenetic analysis, but the dominant genera were consistent with the former results. (2) The species of cyanobacteria in algal crusts were different from each other in the 10 sample sites, but Oscillatoria and Microcoleus were found in each sample site, which proved that they were the dominant genera in algal crusts of Gurbantunggut Desert. In addition, there were more cyanobacteria species in Gur2 and Gur17, and fewer cyanobacteria species in Gur3, Gur5 and Gur9. However, the relative geographical locations of Gur2, Gur3, Gur5 and Gur17 were relatively close, indicating that geographical location was not the main factor affecting the distribution of cyanobacteria. (3) Redundancy analysis results showed that microbial biomass nitrogen (MBN) and soil organic carbon (SOC) have the greatest impact on the diversity of cyanobacteria, followed by nitrate nitrogen (NO^-₃N), microbial biomass carbon (MBC). Total phosphorus (TP) and total potassium (TK) have the least impact. The research showed that the cyanobacteria diversity and physicochemical properties of the soil in different regions of the Gurbantunggut Desert are spatially heterogeneous. The algae crusts in the middle, south of the desert are the most nutritious and the diversity of cyanobacteria is higher, while the algae crusts in the east, west are poor in nutrition, and the cyanobacteria richness and diversity are lower.