Fungi in drylands play a crucial ecological role as facilitators of soil carbon allocation and nutrient availability. However, it remains unclear whether the complex interspecific characteristics of fungal communities in biocrusts are influenced by different environmental factors. Here, at an ideal ecosystem successional study site (almost 65 years), we experimentally investigated whether the structure, diversity and molecular ecological network of fungal communities change with vegetation recovery and succession. Using molecular ecological network analysis and diversity indices, we found that early successional stages, despite lower fungal biomass, were dominated by resilient species such as Filobasidium Their vigorous mycelial growth effectively decomposes recalcitrant organic compounds like lignin, releasing nutrients into the soil. Their developed mycelia can also wrap around soil particles, promoting the formation of biocrusts. In later stages, fungi proliferate, such as Omphalina, forming symbiotic relationships with lichens or mosses to protect and regulate moisture, while obtaining essential carbon sources for growth. Although an increase in positive-to-negative interactions in cooccurrence networks can reduce network stability, it promotes mutualistic interactions that enhance ecosystem functioning. As succession advances, increased fungal diversity and network complexity foster the secretion of metabolites that contribute to soil stabilization, nutrient cycling, and overall ecosystem recovery. Our findings suggest that increasing fungal network complexity and cooperation over time play a critical role in enhancing ecosystem function, particularly in nutrient cycling and soil stabilization, during the later stages of succession. Taken together, this study highlights the critical role of fungal communities in biocrusts as drivers of soil stability, nutrient cycling, and ecosystem restoration, offering valuable insights into their long-term contributions to arid land resilience.