In order to strengthen the water supply safety of Jinze water source which is an important component of the Huangpu River water supply system in Shanghai, meanwhile considering the flood control and water supply demands of Taihu Lake area and Taipu River, this paper studied a multi-objective joint operation of Taipu Sluice and 88 sluice-controlled floodgates along Taipu River. Based on the analysis of present operation modes of Taipu Sluice and floodgates along the river, two kinds of joint operation schemes(10 schemes altogether)were proposed. Then a refined model of water quantity&quality of the Taihu Lake Basin was adopted to simulate the above-said schems, thus setting up the multi-objective functions of flood control, water supply and water environment. Then an ant colony optimization algorithm was used to optimize the above schemes. The results showed that compared with the present schemes, increasing flow discharge by referring to the water level of Taihu Lake and water quality in Jinze section, with the floodgates along the Taipu River under the ordered control, could significantly improve the key water quality index of Jinze water source and obviously elevate the Jinze lowest water level, while the other operation demands of the basin and other regions were barely affected.