[Background] Napahai plateau wetland is located in the northwest of Yunnan province. It is a uniquelow-latitude-high-altitude and seasonal semi-closed plateau wetland in China. Fungi play special roles in the maintenance and stabilization of wetland ecosystems. However, little is known about the fungal community composition and diversity in Napahai plateau wetland. [Objective] To systematically analyze the fungal community composition and diversity a in the soils of Napahai plateau wetland in different seasons and locations and their relationship with the environmental factors, promoting the understanding of microbial diversity in plateau wetlands. [Methods] In this study, fluorescence quantitative PCR and high-throughput sequencing were used to analyze quantity, diversity and composition of fungal community in the soils of Napahai plateau wetland in different seasons and sampling sites, and their association with soil environmental factors was further analyzed. [Results] The results showed that about 60% of the fungal sequences did not exhibit similarity to known sequences. The rest belonged to 6 phyla, 17 classes, 37 orders, 53 families and 63 genera, and most belonged to the phylum Ascomycota and the major dominant genus Gibberella. Taxonomic composition, OTU distributions and beta diversity analysis showed that the diversity and composition of fungal community were more affected by soil types than by season changes, presumably due to different rhizosphere effects and species of plants. CCA (Canonical correlation analysis) showed that the diversity of fungi was almost influenced by soil physiochemical factors in different sampling sites. [Conclusion] Our research revealed the fungal community in the soils of Napahai plateau wetland exhibit unique diversity and composition, emphasizing the importance of protecting and restoring the enviroment of Napahai plateau wetland from the perspective of microorganisms.