The formation and development of algal crust improve soil stability and promote the retention of soil organic matter, which create favorable foundational conditions for soil microbial growth, reproduction and herbaceous plant topology. Hence algal crust potential function is of great significance for the subsequent succession of biological crusts. However, the microorganisms and its potential functions of algal crusts nutrient cycling in Gurbantunggut Desert are still unclear. In this paper, the microbial community, the carbon and nitrogen cycling functional gene characteristics of algal crust in different regions of Gurbantunggut Desert were investigated using metagenome sequencing technology. The results showed that. Cyanobacteria, Proteobacteria and Actinobacteria were the dominant microbial communities in algal crusts and play an important role in desert carbon fixation and nitrogen cycling. The microbial α-diversity results showed that only the richness indices has significantly different among the three regions. β-diversity results showed that microbial communities of algal crusts did not changed due to local climatic and physico-chemical differences in the desert. Microbial community functional genes were more sensitive to environmental changes than microbial community structure. The functional genes of algal crusts in the eastern and western deserts show significant differentiation. The Reductive citrate cycle was the primary pathway of autotrophs for carbon fixation in algal crusts. The Calvin cycle served as the primary pathway of photosynthetic organisms for carbon fixation, where rpiA and rbcS genes were more susceptible to precipitation. Variances in the contributions of Sphingomonas, Nostoc, and Scytonema to the carbon fixation process may potentially underlie the divergence of genes associated with carbon fixation functions.The primary nitrogen cycling pathway in algal crusts were nitrate reduction, and the most nitrogen were assimilated into ammonium by soil microorganisms through nitrate assimilation, and the small amount of nitrogen emit in the form of nitrous oxide and nitric oxide through denitrification. Nitrogen fixation were relatively weak, which only included Nostoc and Scytonema and three functional genes: nifH, nifD, nifK. Moreover, the expression of functional nitrogen fixation genes appears to be particularly influenced by variations in soil nitrate nitrogen content. The nitrification process only annotated to the ammonia monooxygenase or methane monooxygenase encoding by pmoABC-amoABC genes, whereas the hao, nxrA and nxrB genes were not be annotated.