Biocrust fungal communities are typically composed of abundant, intermediate, and rare taxa that collectively sustain critical ecological functions in arid ecosystems through dynamic responses to nutrient fluctuations. However, the compositional and interactive responses of these fungal categories to changing nutrient supply remain poorly understood. In this study, we innovatively employed controlled microcosms to characterize the community structures and co-occurrence networks of abundant (AFs), intermediate (IFs), and rare fungi (RFs) in biocrusts across three nutrient levels (T1: low; T2: medium; T3: high). Alpha diversity was highest in IFs and increased significantly with nutrient supply (P < 0.05), while RF diversity showed no significant change between T1 and T2 (P >= 0.05) but increased significantly from T2 to T3 (P < 0.05). The relative abundance of AFs and RFs increased with nutrient supply, whereas that of IFs declined. Network analysis revealed increased complexity and negative interactions with rising nutrient supply. Keystone hubs shifted from IFs to RFs, with OTU348 (Lep-tobacillium leptobactrum) and OTU392 (Cutaneotrichosporon curvatum) consistently identified as keystone species across all nutrient levels. Moreover, fungal community compositions and network structures were closely associated with soil nutrient supply, particularly total phosphorus, available nitrogen, and available potassium. Our findings provide novel insights into microbial community responses to nutrient supply and establish a conceptual foundation for strategically manipulating fungal keystone taxa based on nutrient conditions to promote ecosystem restoration in drylands.