Biological soil crusts (BSCs) play vital roles in stabilizing desert soils, regulating nutrient cycles, and supporting plant establishment, making their spatial and temporal distribution key indicators of desert ecosystem stability. Using metagenomic sequencing, we analyzed microbial communities in bare sand, algal crusts, and moss crusts in the Gurbantunggut Desert, aiming to elucidate the connections between microbial dynamics and key ecological processes during BSC development to uncover how microscale microbial processes shape broader spatial ecosystem patterns. The three soil types exhibited distinct microbial communities and functional capacities, particularly in carbon fixation and nitrogen cycling processes. Microbial network complexity increased from bare sand to algal and moss crusts,with higher clustering in algal crusts and shorter connectivity paths in moss crusts, both indicating intensified microbial interactions and network cohesion. Algal crusts showed reduced prokaryotic carbon sequestration potential, likely driven by ammonium limitation that suppressed carbon cycling gene expression in heterotrophic taxa (e.g., Actinobacteria), while dominant Cyanobacteria sustained baseline photosynthesis to support early crust development. Differences in microbial nitrogen utilization strategies altered nitrogen cycling dynamics and contributed to niche differentiation among crust types. These shifts reflected strong environmental filtering, which shaped both microbial composition and functional potential across the successional gradient. Source tracking analysis indicates that bare ground was the primary microbial source during BSC succession and that microbial inheritance between crust types was selective rather than continuous. Our findings uncover key mechanisms driving microbial community assembly and succession in desert BSCs, offering new insights for ecological monitoring and restoration in arid environments.