Abstract: The Three Gorges Reservoir has been put into full play in the comprehensive benefits of flood control, hydroelectric power generation. However since the 175 m trial water storage in 2008, the eutrophication in the reservoir area has become an increasingly problem. It is of great significance to clarify the nutrient source of eutrophication succession in the Three Gorges Reservoir, and to put forward an effective total control strategy and refined management scheme. In this paper, taking the Meixi River on the left bank of the Yangtze River in the Three Gorges Reservoir area as a typical tributary, based on the monthly measured hydrological, hydrodynamic and water quality data from 2016 to 2019, we constructed a three-dimensional water environment mathematical model for the Meixi River to study a relationship between the flow in Changjiang mainstream-Meixi River and water qualities in characteristic sections of the tributary. At the same time, we quantitatively analyzed the source composition and structural characteristics of nutrients in the eutrophication section of Meixi River reservoir bay and verified its water environmental capacity under the interaction between mainstream and tributary. Then we put forward a hierarchical total control demand and the limit value of water quality concentration in storage based on hierarchical total capacity control and water eutrophication reduction, and formulated a refined management scheme of water quality concentration of main and tributary to meet the long-term management requirements of Rivers (Reservoirs) Chief System. The results showed that the water environmental capacity of CODMn, TP, and TN in the Meixi River tributary were 18 417, 373 t/a and 7 528 t/a, respectively. Under the constraint that the water quality of each characteristic section in Meixi River reaches the standard, the concentration limits of CODMn, TP and TN that flow into Meixi River reservoir bay were 2.50~6.30 mg/L, 0.052~0.055 mg/L and 1.05~1.10 mg/L, respectively; under the condition that the mild eutrophic state is reduced to the mesotrophic level in the high-incidence area of water blooms in the Meixi River reservoir bay, the concentration limits of CODMn, TP and TN that flow into the Meixi River reservoir bay were 2.00～4.00 mg/L, 0.05 mg/L and 1.00 mg/L, respectively. The research results can provide technical support and reference for the water quality standard management and scientific prevention and control of water eutrophication of tributaries of Three Gorges Reservoir.