Abstract: Quantitative analysis of the topological structure and evolutionary patterns of the National Water Network can provide theoretical support for the high-quality development and spatial layout optimization of this network. This study develops a complex network model of the national water network on the basis of complex network theory. Global characteristics are evaluated through the degree distributions of network structure and flow. Important nodes are identified by means of a fusion centrality index, and an improved InfoMap algorithm is introduced to delineate hydraulic connection zones. The results indicate that inter-basin water transfer has substantially enhanced the connectivity and structural balance of the water network, with the number of nodes with a degree greater than 3 increasing from 30 to 159 and the proportion of low-flow nodes also rising. At present, the proportions of key nodes and hub nodes in the four major river basins, namely the Yellow River, Huai River, Hai River, and Yangtze River basins, have reached 95.1% and 100%, respectively. In addition, the number of hydraulic connection zones across the entire network has decreased from 125 to 104. Overall, water transfer projects have reshaped the connectivity of the water network at the topological level, and the four major river basins of the Yellow River, Huai River, Hai River, and Yangtze River have formed highly coupled hydraulic connection zones. In the future, the security of the water network urgently requires a transition toward coordinated and resilient management at the scale of the entire network.