According to the input-output tables of Jiangsu-Zhejiang-Shanghai area in 2002, 2007 and 2012, using the social network analysis its industrial linkage network is formulated from the perspective of water resource input-output. The relevant indices such as characteristic path length, clustering coefficient, centrality and cohesive subgroup are calculated, and the industrial linkages in the total Jiangsu-Zhejiang-Shanghai area and various provinces and city are compared and analyzed. The results show that there is a small-world property and high network density with close industrial linkage. The chemical industry representing the industrial sector is of outstanding centrality and is the central industry in the area, and the status of service sector has increased, but the disproportion is even more prominent. Now eight cohesive subgroups are formed, and the linkage between their industrial sectors, which indicates the trend of development is clustering. Some suggestions are put forward in order to promote the balanced and sustainable development under water resource constraints, such as saving and using water intensively on central industry, improving the utilization of water resources, formulating different policies on water resources and promoting industry integration.