Fertilization plays important roles in sustaining crop yield and quality, and soil microbial community and composition. However, little is known about the soil fungal communities in tea plantation soils, even though tea plantations constitute significant land use in South China. The diversity and distribution of soil fungal communities are significantly influenced by soil physical-chemical properties and field management. Therefore, this study sampled the surface layer (0-10 cm) and the sub-surface layer (10-20 cm) soils from a tea plantation in the Puer area, Yunnan Province, China. The experiment consisted of three different treatments. These were no N application (CK), chemical N fertilization with 300 kg/hm² N(N300), and combined inorganic and organic fertilization (30% N in organic form, OM30). Soil DNA was extracted from the soils for PCR amplification and high throughput sequencing in order to study the effects of organic and inorganic fertilization on the fungal communities of the tea garden soil. The results showed that the surface layer (0-10 cm) α-diversity of the fungal community, the Chao1 richness index, and the Shannon diversity index values were significantly higher than those recorded for the sub-surface layer (10-20 cm) (P < 0.05). Within the same layer, the α-diversity tendency was CK > N300 > OM30. Relative abundance at the phylum level showed that Ascomycota, Basidiomycota, and Zygomycota were the three dominant phyla in the experimental soil and Sordariomycetes, Tremellomycetes, and Mortierellomycotina were the three dominant Ascomycota, Basidiomycota, and Zygomycota classes, respectively. The relative abundances of Ascomycota and Basidiomycota were higher in the surface layer, whereas Zygomycota were relatively more abundant in the sub-surface layer (P < 0.05). The N300 and OM30 treatments increased the relative abundance of Zygomycota, but decreased the relative abundance of Ascomycota within the same layer. Redundancy analysis (RDA) showed that the compositions of the soil fungal communities in the two different layers were driven by several soil physical-chemical proprieties. The Monte Carlo permutation test showed that the carbon:nitrogen ratio and the soil organic carbon, total nitrogen, total potassium, and available potassium content can significantly influence the composition of the fungal community. However, soil pH, which is an important environmental factor, did not have any significant effect on the soil fungal community in this experiment.