In order to study the water connectivity in the main urban area of Yangzhou, this paper extracts the water system based on the method of graph theory edge connectivity and uses GIS technology to establish the water system graph model of the main urban area of Yangzhou and calculate the water system edge connectivity. The results show that the water connectivity of the main urban area of Yangzhou is 2. The key sections affecting the overall connectivity of water system include the section from the junction of Qili River and Shashi River to the ancient canal, the section from the junction of Yiyang River and Zhaojiazhigou to the Xiyingou, the section from the Lanyue River to Zhaojiazhigou, and the section from the junction of Laosha River and Shashi River to Qujiang Park. The key gates and dams are Yangzhou Gate, Golden Dam Gate, Pingshantang Pumping Station and Mingyue Lake Gate. After the four gates are closed, the overall connectivity is reduced by 50%. Measures such as river dredging, ecological slope protection, and sluice control can be used to improve the water connectivity in the main urban area of Yangzhou.