Deserts, as typical extreme ecosystems, harbour unique microbial communities with remarkable environmental adaptability and biotechnological potential. This review systematically summarizes recent advances in understanding desert microbial diversity, functional mechanisms, and resource utilization. By integrating high-throughput sequencing, multi-omics approaches, and innovative cultivation technologies, we elucidate microbial adaptation strategies under extreme stressors and propose an integrated “diversity-function-application” research framework. Studies have revealed that desert microorganisms produce a range of bioactive compounds with antibacterial, antitumour, and anti-radiation activities, demonstrating broad application prospects in pharmaceuticals, agriculture, and industry. Furthermore, these microbial communities play critical roles in carbon and nitrogen cycling, ecological restoration, and responses to global changes. Although traditional cultivation methods have limited access to the vast “microbial dark matter”, interdisciplinary technological integration is gradually overcoming this bottleneck. Future research should prioritize the construction of microbial resource banks, in-depth functional gene mining, and the transformation of green biotechnologies to provide scientific and technological support for addressing global challenges.