Rocky desertification area in Western Hunan province is a fragile and sensitive area of ecosystem in China. Soil microorganisms play an important role in maintaining the stability of forest ecosystem structure and function in rocky desertification area. Thirty two year-old pure Pinus massoniana forest, pure Betula luminifera forest and mixed Pinus massoniana and Betula luminifera forest in rocky desertification area with the same site conditions were selected as the research objects. The non-forested shrub grassland with the similar site conditions was taken as the control to compare and analyze the influence of different afforestation modes on soil fungal community structure and diversity and their main driving factors. The composition and diversity of soil fungal communities in three forests were analyzed by Illumina HiSeq second-generation high-throughput sequencing technology. The results showed that the dominant groups of soil fungi were different under different afforestation modes. The dominant phylum of soil fungi in Betula luminifera, mixed forest and non-forested shrub grassland were Ascomycota, and the relative abundance was the largest in non-forested shrub grassland, which was 64.0%. Basidiomycota was the dominant group in Pinus massoniana, its relative abundance accounted for 57.9%. The total number of soil fungal species and Shannon index of mixed forest were significantly higher than those of Pinus massoniana and Betula luminifera forest. On the whole, the diversity of fungal community was as follows:non-forested shrub grassland > mixed forest > Pinus massoniana forest > Betula luminifera forest. The contents of soil organic carbon (SOC) and total nitrogen (TN) in the mixed forest and Betula luminifera pure forest were significantly higher than those in non-forested shrub grassland. Mantel test showed that fungal community structure was significantly correlated with total phosphorus (TP), SOC, ammonium nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃^--N), TN, pH and water content (SWC) (P<0.05). Soil SOC, TN and pH had the greatest impact on fungal community structure. Redundancy analysis (RDA) showed Ascomycetes were positively correlated with pH, TP, SOC, TN, AP and NO₃^--N content; Basidiomycetes and Mortierella were mainly positively correlated with NH₄⁺-N, and negatively correlated with pH, TP, SOC, TN, AP and NO₃^--N. There was a positive correlation between Rozellomycota and SWC. In conclusion, compared with pure coniferous forest, coniferous and broad-leaved mixed forest in rocky desertification area can significantly improve the diversity of fungal community by increasing soil SOC and TN, and promote the improvement of soil fertility. The results can provide basis for artificial vegetation restoration and soil fertility management in rocky desertification area.