In recent years, the eutrophication in the typical tributaries of the Three Gorges Reservoir has attracted widespread attention. In the present paper, three typical eutrophic tributaries in the Three Gorges Reservoir area, that is, Xiaojiang River (Pengxi River), Daning River and Xiangxi River, were selected for research, and a two-dimensional hydrodynamic and water quality coupling model that is for the area from Zhutuo to dam site was constructed by using MIKE 21 software. On this basis, the temporal and spatial distribution of pollutants in three tributaries in 2021 was further simulated and analyzed. The results showed that: (1) The coupling model after calibration and validation had good simulation accuracy for hydrodynamic and water quality indexes in the reservoir area, and the simulation effect was in good agreement with the measured results; (2) The concentration of each pollutant was closely related to the change of water level and water quantity. From the highstand period to the pre-discharge stage (January-June), the concentrations of total nitrogen and total phosphorus increased, which were very high from the post-discharge period to the lowstand period (July-September); (3) The concentration of pollutants in the confluence of the main stream and tributaries was high due to the backward flow of the main stream. To sum up, the higher concentration of pollutants and the higher water temperature in spring and summer were conducive to the rapid reproduction of algae and other plankton, resulting in eutrophication, and the algal bloom was easy to break out in the reservoir area. During the water storage period and highstand period (October-December), the concentrations of total nitrogen and total phosphorus showed a downward trend, mainly due to the self-purification of water and the degradation of pollutants. The research conclusion can provide a reference for water quality evaluation, water supply safety and pollutant treatment in the Three Gorges Reservoir area.