The elevational distribution pattern and maintenance mechanism of biodiversity are critical issues for the comprehensive study of biodiversity and ecosystem functioning. Compared with macroorganisms, we know very little about the patterns of microbial diversity across elevational gradients, though microbes drive many important biogeochemical cycles on earth. In this paper, we used Illumina Miseq high-throughput sequencing technology to comprehensively analyze the variation characteristics of soil fungal community composition and diversity in the subalpine ecosystem of Mount Wutai (altitude of 2000-3058 m above sea level). The results showed that Ascomycota, Basidiomycota Zygomycota, Chytridimycota were the dominant soil fungal phyla. Non-metric multidimensional scaling (NMDS) and similarity analysis (ANOSIM) indicated that the compositions and structures of fungal communities were significantly different among the elevation gradients (P<0.05). Canonical correspondence analysis (CCA) showed that there were significant correlations between pH, plant richness and total carbon content and soil fungal community structure (P<0.05). There was a significantly positive correlation between soil fungal diversity and plant diversity (α and β-diversity) at local elevation scale (P<0.05). Variance partitioning analysis (VPA) and partial Mantel analysis showed that both environmental factors and spatial variables played roles in the assembly of soil fungal community, and environmental factors were dominant. The Bray-Curtis distance between soil fungal communities was significantly and positively correlated with the elevation distance (P<0.05), indicating that environmental selection was the determinant of the elevation distribution pattern of soil fungal communities. In conclusion, there were significant differences in the structure and diversity of soil fungal communities along the elevation gradient of Mount Wutai, and the assembly mechanism of fungal communities was mainly determined by deterministic processes. The soil pH, plant richness and total carbon content may be the most important factors affecting the soil fungal community structure.