To reduce the impact of Fluctuating Zone, the Three Gorges Reservoir pre-dam is rare in the world which is specially designed and is the largest artificial lake body in China. The ecological benefits of landscape, farmland and lake and the social benefits of livable city have been significantly enhanced since the successful commissioning of the Hanfeng Lake pre-dam system. The paper proposed the application of layered hydrology and water quality monitoring for analysis of Tributary runoff and lake body section in the pre-dam commissioning in the whole year, and a total of 17 measured indicators inlucding hydrological parameters such as v, H, etc, physical parameters such as T, pH, SD, DO, TSS etc. and chemical parameters such as permanganate index, Chl-a, TN, DN, NO3--N, NH4+-N, NO2--N, TP, DP, SRP etc. We found that the water quality was poor during beginning drain and impoundment period and was the worst in tributary inflow section of South River, while the best water quality was located in water section of regulating dam in February and October. The TLI Water Quality Evaluation and factor analyses performed have shown that the water body of Hanfeng Lake was slightly eutrophicated, and the main pollution indicators included DN, TN, NO3--N, TP. By the control of pre-dam in three Gorges to eutrophication in commissioning, we found that the average Chl-a reduction effect reached up to 57.73%, the average reduction rate of permanganate index was 28.12%, SRP, TP, TN, TSS, NO2--N, DN, DP etc. were on average cut down by 20.15%-22.81%, the average reduction rates of NH4+-N and NO3--N were 16.92%-18.74%, and the average eutrophic index of water body was reduced by 15.74%. The highest reduction average rate in lake form period appeared from January to March and October to December, and the lowest in river form period was during May to August.The analysis results showed that the commissioning of pre-dam was good and remarkable for controlling eutrophication, and cutting the concentrations of pollutant water storage in the Three Gorges.