In order to explore the reasons of changes in inflow fluxes of total nitrogen and total phosphorus into Taihu Lake, the correlations between the inflow fluxes and the rainfall in the upper reaches of the Taihu Basin were analyzed, and the main sources of total nitrogen and total phosphorus were clarified. Results showed that the average annual rainfall in the Taihu Basin was 1 322 mm from 2010 to 2019, which was 15% higher than that from 1986 to 2009. From 2010 to 2019, the annual rainfall values in the Huxi and Zhexi sub-watersheds were 1 263 mm and 1 552 mm, respectively. From 2010 to 2019, the average annual inflow fluxes of total nitrogen and total phosphorus into Taihu Lake were 32.400 t and 1 800 t, respectively, which mainly originated from the Huxi and Zhexi sub-watersheds. Significant positive correlations were found between the inflow fluxes of total nitrogen and total phosphorus into Taihu Lake and the annual rainfall in the Taihu Basin, Huxi sub-watershed, and Zhexi sub-watershed. Due to the differences in land use, the responses of the inflow fluxes of total nitrogen and total phosphorus to the rainfall in the Huxi sub-watershed were greater than those in the Zhexi sub-watershed. The large amounts of urban and agricultural non-point source pollutants were the main sources of inflow nitrogen and phosphorus into Taihu Lake, and part of the combined rain and sewage into rivers was also one of the sources of the nitrogen and phosphorus pollution loads.The increase of rainfall, especially heavy rainfall in the Huxi and Zhexi sub-watersheds,not only increased the non-point source pollution loads, but also reduced the hydraulic retention time of the upper river network, leading to the decrease of the self-purification capacity of water bodies and the increase of the inflow fluxes of total nitrogen and total phosphorus into Taihu Lake.