Nonpoint source pollution entering rivers will pollute water quality, degrading the health of aquatic ecosystems. However, owing to the lack of quantitative research on the effects of nonpoint source pollution on the structure of aquatic food webs, there is a lack of quantitative basis for river management. Nonpoint source pollution is not only difficult to control effectively, but also the success rate of water ecological restoration projects is low. With the increasing proportion of nonpoint source pollution in water environmental problems, it is urgent to quantitatively assess and predict the impact of nonpoint source pollution on the structure of food webs. Therefore, this thesis presents a method for quantitatively assessing and predicting the impact of nonpoint source pollution on the structure of food webs through using fuzzy clustering to screen the typical points of the impact of nonpoint source pollution, then using canonical correspondence analysis (CCA) and partial least squares regression analysis to comprehensively filtrate the driving factors affect food web that results in nonpoint source pollution, and then determining the impact of each driving factor on the structure of food webs. Finally, the change trend of food web structure is predicted. The results show that (1) the driving factors that the nonpoint source pollution that affects the food web structure is NH3‐N and chemical oxygen demand (COD). The increase in NH3‐N and COD promotes the growth of phytoplankton, causing the change of the primary productivity of the ecosystem, and ultimately changes the entire food web structure; (2) NH3‐N and COD affect the stability, maturity, connectivity and complexity of the aquatic food web structure. The increase of NH3‐N increases the connectivity and maturity of the food web structure but reduces complexity and stability; the increase of COD increases the connection of the food web structure, while reducing the other three indicators; (3) in some areas with good water quality, aquatic species diversity is high, the relationship of interspecies dietary is complex, food web structure level index is high and the structure of food web is stable. The food web structure in the rainy season will be better than that in the dry season. In some areas with severe water pollution and poor food web structure, the ability of the food web to resist external interference is weak. The food web structure in the rainy season will be worse than that in the dry season owing to rainfall into the river. The methods and conclusions in this treatise can provide a reliable and quantitative scientific basis for river ecosystem management and ecosystem restoration and can improve the success rate of ecological restoration projects.