In order to quantitatively reveal the influence of the implementation of the contour interception project on water system structure and function in the river network area in Donghai County, taking the Longliang River-Shian River network area in Donghai County as the research object, a comprehensive analysis method of water system structure and connectivity at regional and nodal levels was proposed based on the analysis method of water system morphological structure, graph theory and landscape ecology method, and complex network method. The morphological structure and connectivity changes of the river network area water system before and after the implementation of the contour water interception project were calculated. The results showed that, in terms of water system structure, the number and length of rivers increased by 76.39% and 77.95%, respectively, after the implementation of the contour interception project; in terms of regional connectivity, the contour interception project connected isolated river networks laterally, increasing the water system circularity, node connection rate, and hydrological connectivity indexes of the regional water network by 101.29%, 37.27%, and 35.23%, respectively, and significantly improving the overall structural connectivity of the water system. The nodal function connectivity was significantly improved, and the spatial distributions of node propagation ability and node importance were optimized due to the bidirectional connection ability of the contour interception project.