Using Illumina MiSeq high-throughput sequencing technology for ITS region of fungi, combined with NMDS, RDA and Mantel test analysis, the differences in the composition and diversity of rhizosphere soil fungi community of the different fertilization levels of no fertilization (0NP), low nitrogen and phosphorus (LNP) and high nitrogen and phosphorus (HNP) under the three cropping modes of Hulless barley monoculture (Q), pea monoculture (W) and hulless barley and pea mixed cropping (Q×W) were investigated, soil physiochemical properties and their correlation with the rhizosphere soil fungi community structure were also analyzed. The results show that soils are alkaline under the three cropping modes, and soil physicochemical properties are significantly different under different fertilization levels. A total of 18 fungal groups are detected under different treatments. Ascomycota (63.5%-78.5%), Mortierellaomycota (3.6%-14%) and Basidiomycota (1.1%-6.9%) are the common dominant groups. At the genus level, Penicillium and Mortierella have the highest relative abundance in the mixed rhizosphere soil of hulless barley and pea, which may be the main fungal communities driving the conversion of organic nitrogen and phosphorus into inorganic nitrogen and phosphorus in soil. Bipolaris, Blumeria, Fusarium and Cladosporium are the four potential pathogenic fungi genera with the highest abundance in soil fungal community, and the relative abundance in the rhizosphere soil of hulless barley and pea mixed cropping is lower than those of hulless barley and pea single cropping. There are significant differences in the relative abundance of the four potential pathogenic fungi under different fertilization levels in the mixed cropping mode. Under LNP and HNP levels, the indices of fungus richness (ACE, Chao1) and diversity (Shannon, Simpson) are lower in rhizosphere soil of mixed cropping mode than those of hulless barley monocrop, while the indices of fungus richness (ACE, Chao1) are significantly lower under mixed cropping mode than those of 0NP level. However, the diversity (Shannon, Simpson) index is higher than the level of 0NP. According to the relative abundance of fungi community at the genus level under different treatments, the mixed cropping pattern can significantly increase the relative abundance of beneficial fungi in rhizosphere soil. Through the analysis of the dominant population and α diversity of microorganisms in rhizosphere soil, compared with hulless barley monoculture and pea monoculture, the mixed cropping pattern of hulless barley and pea can increase the relative abundance of Penicillium, Mortierella and other phosphorus-soluble and ammoniating fungi in rhizosphere soil at genus level, reduce the relative abundance of Bipolaris, Blumeria, Fusarium, Cladosporium and other potential pathogenic fungi groups. Correlation analysis shows that available nitrogen, available phosphorus and organic matter are the main driving factors affecting the difference of rhizosphere soil fungal community structure.