AimsThe vegetation in the Mu Us Sandy Land is characterized by a mosaic distribution of perennial semi-shrubs and biological soil crusts (BSCs). BSCs fulfill essential ecological functions, including soil and water conservation, as well as carbon and nitrogen fixation. This study investigates the mechanisms driving microbial community assembly and the evolution of multifunctionality in BSCs under nutrient limitations in arid and semi-arid regions.MethodsBSCs were collected from different successional stages using a space-for-time substitution approach in the Mu Us Sandy Land. Third-generation PacBio Sequel single-molecule real-time sequencing and bioinformatics analyses were employed to examine the dynamics and variations in the ecological functional structure of microbial communities within BSCs associated with Artemisia ordosica shrub habitats.ResultsUnder prolonged drought in sandy environments, soil P and K are key factors influencing spatial shifts in BSC microbial community succession. Each stage of BSC succession is marked by distinct dominant microbial groups. In the mature stage, microbial diversity and community structure in moss crusts show a stronger preference for specific moss types; for instance, Acidobacteria and Ascomycota are most abundant in Bryum argenteum and Didymodon vinealis, respectively. Soil microbial diversity is the primary driver of the evolution of BSC multifunctionality, with moss type serving as a secondary factor.ConclusionsIn carbon and nitrogen-limited sandy soils, microbial communities influence BSC succession and contribute to material cycling within crust layers. During the mature stage, microbial communities and mosses jointly promote the diversification and stability of BSC ecological functions.