Background and aimsBiological soil crusts (BSCs) are essential components of arid and semi-arid ecosystems, playing a vital role in carbon and nitrogen cycling. However, the variation in microbial community composition and metabolic functions across different BSC types and developmental stages remains poorly understood.MethodsIn this study, we analyzed the functional genes involved in carbon and nitrogen cycling across three representative types of BSCs-algal, lichen, and moss crusts-collected from three major desert regions in northern China. Using metagenomic sequencing, we analyzed the microbial communities and their functional genes.ResultsAlgal crusts have the highest abundance of photosynthetic carbon fixation genes (e.g., RuBisCO and phosphoribulokinase), which decline with BSCs succession, while chemolithoautotrophic genes (e.g., cutM, coxM) are also enriched in algal crusts, suggesting diverse CO2 fixation pathways. Lichen crusts exhibit the highest nitrogen fixation gene abundance (e.g., nifH, nifD, nifK), and nitrogen transformation genes (hcp, narH) are notably enriched in lichen crusts, indicating active nitrogen turnover and potential denitrification. Taxonomic shifts from cyanobacteria to more diverse bacterial communities reflect microbial succession patterns along BSCs development.ConclusionThis study highlights the distinct functional potentials and ecological roles of microbial communities in different BSC types, emphasizing their importance in biogeochemical cycling and ecosystem functioning in desert environments. These findings provide a scientific basis for ecological restoration and management of desertified landscapes.