The aquatic fungal community is highly responsive to lake changes and greatly contributes to biogeochemical processes in lake ecosystems. Based on high-throughput sequencing, we analyzed characteristics of aquatic fungal community structure and diversity at different areas from the Yamzhog Yumco Lake, Kongmo CO Lake, and Chen CO Lake. The results showed that the physicochemical properties of the water were different among the different areas. The fungal community was mainly composed of Ascomycota, Mortierellomycota and Basidiomycota. The results of α-diversity index analysis showed that the operational taxonomic units (OTU) number was significantly higher (P<0.05) in coastal area of Yamzhog Yumco Lake than that in Yamzhog Yumco Lake center water, others α-diversity index were no significant differences between the different areas. Non-metric multidimensional scaling (NMDS) analysis showed that the β-diversity of the fungal communities were significantly different among the different areas (P<0.05). The results of the agglomerative clustering analysis showed that the aquatic fungal community structure was different between the various sites on each area, aquatic fungal community structure was similar among the interchange between Kongmo Co Lake and Chen Co Lake. Statistical analysis indicated that turbidity (NTU), chemical oxygen demand (COD), ammonia nitrogen (NH₄⁺-N) and total nitrogen (TN) were significantly positive related to aquatic fungal richness among different sites. The total phosphorus (TP) and NH₄⁺-N were important factors influencing the community structure of aquatic fungal in the Yamzhog Yumco Lake. The aquatic fungal community from Yamzhog Yumco Lake showed high species richness, hydrologic conditions and anthropogenic influenced were important factors for the aquatic fungal community.