Biological soil crusts (BSC), known as “desert ecosystem engineer”, play an important role in the restoration and stability maintenance of desert vegetation. BSC microbial communities are the main components of their functions. They participate in the formation of BSC, the improvement of soil physiochemical properties, the stability of soil aggregates and the development of vegetation. In the early stage, due to the limitation of technical methods, the mechanism of how BSC microbial communities regulate the stability of desert vegetation is unclear. However, with the rapid development of soil microbiome technologies in recent years, the research on the composition and function of BSC microbial communities has made great progress, and the contribution of BSC microbial communities to desert ecosystem has a clearer understanding. In this paper, the compositional structure of bacterial, fungal and archaeal communities and their potential functional changes in the carbon and nitrogen cycles during BSC succession in temperate desert are reviewed. Additionally, the soil environmental factors affecting the structure and function of microbial communities are summarized, and the successional model of interaction between different BSC microbial groups and soil physiochemical properties is explained. These results help us to clarify the mechanism of BSC promoting the improvement of desert soil conditions, and to provide theoretical basis for understanding the restoration process of desert vegetation and the contribution of temperate desert ecosystems to the world.