For the Gongming Reservoir-Qinglinjing Reservoir connection project in the Pearl River Delta water resources allocation project, a hydrodynamic-water quality-ecological coupled model for this connection project was established based on measured water quality and meteorological data, as well as future climate model data, by using the GOTM reservoir hydrodynamic model and the GOTM-FABM-WET reservoir ecological dynamics model. The hydrodynamic characteristics and water quality response laws of the connection project under different operation modes were simulated, and the eutrophication evolution trends of the reservoirs from 2022 to 2031 under two climate change scenarios (SSP1-2.6 and SSP3-7.0) were predicted. The results indicate that after connection, the total nitrogen mass concentration in the receiving Qinglinjing Reservoir shows a seasonal reversal characteristic of increasing from January to July and decreasing from July to December. Meanwhile, the total nitrogen mass concentration in Gongming Reservoir decreases slightly, and the changes in chlorophyll a and total phosphorus mass concentrations are relatively small. Under the background of climate warming, the chlorophyll a mass concentration in both reservoirs is expected to reach 30-40 μg/L after 10 years of the connection project operation, and the trophic level index (TLI) enters the mild eutrophication range (50-60). Moreover, under the high-emission scenario, the total nitrogen mass concentration in Gongming Reservoir faces the risk of exceeding the limit of the Class Ⅲ water quality standard.