[Objective] To explore the relationship between soil fungal community structure and soil environmental factors of the degradation process of alpine grassland in Qilian Mountains.[Methods] We analysed the changes and diversity of fungal community structure in lightly, moderately and severely degraded grassland by Illumina Miseq PE250 high throughput sequencing technology, and redundancy analysis (RDA) of the relationship between soil fungal community structure and soil environmental factors was analysed.[Results] With the aggravated degree of deterioration, soil pH was increased, electrical conductivity was increased first and then decreased, soil water content, organic carbon, total nitrogen, total phosphorus and total potassium were gradually decreased. We obtained a total of 750575 effective sequences and 5788 OTUs by high throughput sequencing, the Chao1 and Shannon-Wiener index of fungal communities varied in different samples. The fungal communities' dominant phyla of all soil samples were Ascomycota, Basidiomycota, Zygomycota, Glomeromycota and Chytridiomycota. RDA analysis showed that soil available potassium, total nitrogen, available nitrogen and organic carbon were the important driving factors for the distribution of soil fungal community structure in different degraded alpine grassland of Qilian Mountains.[Conclusion] The soil fungal community structure was significantly different in different degraded alpine grassland, and soil environmental factors was a important factor influenced the distribution of soil fungal community structure in Qilian Mountains.