Abstract: The traditional water system connectivity scheme is mainly dominated by the water system structure, ignoring the influence of connectivity on water system function. In the layout of the urban water system, the connecting structure and function of the water system are integrated to formulate the connecting scheme of the water system. Based on the centrality evaluation method, a method is proposed to quantitatively portray the importance of river segments. The functional relationship between the connectivity function and its characterization parameters is established with the help of the affiliation function, and the effect of the water system connectivity function is quantified accordingly. The two-stage optimization model of the water system connectivity scheme with structure-function coupling is established with the river network connectivity function achievement rate. The objective is to determine the effectiveness of the water system connectivity, and based on this, the optimal joint gate scheduling scheme is selected. Taking the Qingyi River as an example, the study shows that the overall connectivity of the water system of Qingyi River in the original river network is good, but the connectivity near the Hucheng River and Yinma River is poor. Improving the Hucheng River-Qingni River and the Yinma River-Xiaohong River connections could greatly enhance the connectivity of the water system near the Hucheng River and Yinma River.