Abstract: Water system connection projects are of great significance to the conservation of ecological environment and the development of social economy of the connected areas. In order to clarify the water diversion and drainage effect of the projects,taking the Yangtze River to Chaohu Lake Water Diversion Project as an example,the evaluation index system of “structure-environment-ecology-economy ”（ SEEE） is constructed to evaluate the influencing effect of the water system connection project on the connected areas,and to analyze the temporal and spatial variation characteristics of the comprehensive effect index. The results show that the correlation strength of water system connection to the four subsystems decreased successively,the composite effects of connected areas on different spatial scales（ Lujiang County,Chaohu City,Hefei City and Chaohu Lake Basin） were hierarchical,and the comprehensive effect index of each area fell into the range of 0. 39-0. 57,which decreased with the increase of the spatial scale. The connectivity effect of 2008-2018 followed the law of diminishing marginal effect and had a certain lag effect. The results can provide a theoretical reference for the construction of water system connection projects.