Understanding the relationship between soil fungal communities and soil function is vital to establish a sustainable and ecologically friendly tea (Camellia sinensis L.) cultivation. However, there is limited research on the response of soil fungal communities to tea-fungus intercropping, particularly how it is related to soil biodiversity and fertility. Here, we assessed and compared the fungal communities using a metabarcoding technique, soil properties in three plantations (1, 2, and 5 yr of tea-Pleurotus intercropping plantations), and a 5 yr chemically fertilized monoculture plantation. We obtained a total of 3493 operational taxonomic units (OTUs) from four tea plantations. Five hundred and ninety-three fungal OTUs are shared by all plantations, and the other 471 fungal OTUs are shared by three plantations. The largest number of OTUs was recorded in 5 yr tea-Pleurotus intercropped plantations (N = 2040), followed by 2 yr (N = 2024) and then 1 yr (N = 1471), while the chemically fertilized plantation recorded 1823 OTUs. Tea-Pleurotus intercropping showed a significant effect on the increased diversity of soil fungal diversity compared with the monoculture tea cultivations. Fungal groups Basidiomycota, Ascomycota, and Mortierellomycota were the most abundant taxonomic groups recorded in all soil samples. Principal coordinate analysis revealed that fungal community composition in tea-Pleurotus intercropped plantations and monoculture tea plantations was significantly different. Besides, redundancy analysis revealed that soil nutrients significantly influence soil fungal community composition. Our results demonstrate that tea-Pleurotus intercropping may offer long-term benefits to soil biodiversity and sustainable benefits in the tea plantations.