[Objective] To study wolfberry rhizosphere fungal diversity in different regions, we attempted to explain the correlation between Ningxia wolfberry quality and soil microbial flora from the perspective of rhizosphere fungal community.[Methods] We used the miseq high-throughput sequencing method to analyze the Internally Transcribed Spacer (ITS) region in the rhizosphere soil samples of Lycium barbarum L. in four different regions of China. We analyzed Alpha diversity, Beta diversity and fungal community structure, and determined the main active ingredients of Lycium barbarum L. in the four regions, and analyzed the correlation between the quality of Lycium barbarum L. and soil physical and chemical factors and the diversity of rhizosphere fungi.[Results] Polysaccharide and betaine of Lycium barbarum L. in Zhongning were higher than Jinghe's and Xingren's, and Golmud's was the lowest. Species diversity and structure analysis of soil fungi in the rhizosphere of Lycium barbarum L. showed that species diversity and structure were similar in Jinghe, Xingren and Zhongning, Ascomycetes and Zygomycota accounted for about 80% of the total species, but Golmud's was different from other regions, ascomycetes accounted for 58% and Chytridiomycota and Neocallimastigomycota were much higher than the other three regions, nearly 25% of the proportion of total fungi. Beta diversity analysis showed that the similarity of fungal flora structure in the rhizosphere soil of the Lycium barbarum L. in four regions was Xingren, Jinghe, Zhongning and Golmud.[Conclusion] The research showed that the composition of fungal species in rhizosphere soil of Lycium barbarum L. was abundant and there were some differences in the population structure of soil fungi in the rhizosphere soil of different regions. Some active ingredients of Lycium barbarum L. had a certain correlation with the population structure of soil fungi in the rhizosphere. So, microorganism boost the growth and quality of Lycium barbarum L..