Abstract: Soil fungi is an important promoters for material circulation and energy flow in ecosystems. In order to explore the community structure and influencing factors of soil fungi in different forest types in karst hills among depression in Southwest China, soil samples from three typical forests (shrub, secondary forest and primary forest) were selected for fungal ITS high-throughput sequencing. The results showed that the soil physical and chemical properties in shrub forest and primary forest were closest, with high nutrient content. A total of 2,013,410 valid sequences and 9677 OTU were obtained from the 33 soil samples, which belonged to 18 phyla, 59 classes and 946 genera. Soil fungi were composed of Ascomycota, Basidiomycota, unclassified fungi, Mortierellomycota, and Rozellomycota, in all the three forest types. Among them, Ascomycota and Basidiomycota were the dominant soil fungi in three forest types, which together accounted for nearly 80% of the total fungal abundance. The primary forest and shrub forest had the higher α diversity with the closest fungal community composition and structure. LEfSe analysis showed that the key dominant fungal groups were different in each forest. Specifically, the biomarkers were Sordariomycetes, Eurotiomycetes, Eurotiales, and Nectriaceae in the shrub forest, Agaricomycetes and Archaeorhizomycetes in the secondary forest, while unclassified Agaricales and Inocybaceae in the primary forest. Correlation analysis showed that soil fungi were closely related to soil physical and chemical factors. Redundancy analysis further showed that exchangeable Ca2+, Mg2+, total potassium and temperature had great effects on the soil fungal distribution of soil fungal, which were the dominant factors affecting the soil fungal community structure and distribution in karst forests.