Unraveling soil microbial community assembly mechanisms is critical for understanding community distribution patterns. This study investigated soil fungal community characteristics, assembly processes, and their responses to environmental factors in wetlands of the Tarim River Basin. Key findings revealed: (1) Under environmental stress, fungal communities exhibited significant structural divergence with narrowed ecological niches, demonstrating specialization. Specialists dominated with significantly higher relative abundance, while only a few taxa as generalists were widely distributed; (2) Saprotrophic fungi were the dominant functional group. Specialists included more multiple trophic modes, and plant pathogens rarely occurred as generalists; (3) Specialists exhibited higher environmental sensitivity and distinct habitat preferences, while generalists demonstrated greater stability and potential resistance. Notably, the prevalence of generalists may contribute to community homogenization, yet it simultaneously enhances functional redundancy within the ecosystem; (4) Community assembly was primarily governed by stochastic processes, though homogeneous selection significantly contributed at local scales. Specialists intensified dispersal limitation, while generalists were dominated by ecological drift and enhanced homogeneous selection. Environmental stress further promoted the local aggregation of specialists, whereas it primarily enhanced environmental filtering for generalists. Collectively, under environmental stress, soil fungi occupying distinct niches may have completely different corresponding patterns and play different roles to maintain ecosystem functioning.