Water system connectivity is an important measure to optimize the balanced spatial allocation of water resources and water security patterns. Inland river basins in arid zones are generally insufficiently connected, so the scientific evaluation of the current status of water system connectivity and the centrality of its nodes in the water system network has practical significance for the scientific construction of regional water networks. Taking the Tarim River Basin in Xinjiang, China, as an object, this study conducted a comprehensive evaluation of basin water system connectivity by constructing a water system connectivity evaluation system with a total of 12 indicators for the three aspects of pattern connectivity, structural connectivity and functional connectivity. Subsequently, the TOPSIS model, with combined weights of the analytic hierarchy process and the entropy weight method, was used to comprehensively evaluate the connectivity of the watershed’s water system. The research evaluated the node centrality of the water system network that was closely related to the basin water system connectivity by using complex network analyses. The study results indicated the following: (1) among the source streams in the Tarim River Basin, the connectivity of the Aksu Basin was the best and that of the Keriya Basin was the worst and (2) the distribution patterns of the eigenvector centrality and betweenness centrality of the basin hydrological network nodes were similar, with nodes of highest centrality concentrated in the vicinity of the mainstems and the source–mainstem intersections. This work provides a basis and reference for the construction of water system connectivity and the selection of key control sections for ecological flow in the Tarim River Basin.