Yangtze River economic zone, as China’s key strategic zone, is closely related to national development by its ecological restoration and resources use. Jiangsu’s chemical industry, an intensive polluting and resources-depleting industry, needs to properly handle industrial development and resources & environmental protection, which is of significance to protect Yangtze River and realize carbon reduction. This paper establishes a multiple-objective optimization model of chemical industry under dual constraints of carbon reduction and water ecological carrying capacity, and applies NSGA-II-VIKOR algorithm to discuss the way to adjust Jiangsu’s chemical industrial structure. Balanced development scenario, compared with low-carbon, water-saving and economic development scenarios, can save water of 998.48×10⁴  m3 , reduce carbon emission intensity by 4.27%, and make GDP rising rate up to 4.73% on the basis of benchmark year 2017. Water resources are used efficiently and carbon emission is largely reduced, while economy gains high-quality development. Chemical industrial structure needs to be adjusted through developing rubber and plastics, limiting petroleum processing, coking coal and nuclear fuel processing, using water-saving and carbon-reducing measures in chemical fiber manufacturing. Optimization of chemical industry needs to promote clean energy and reform energy consuming structure, with coal use down by 5.54% and gas & electricity use up by 5.45%. Water resources allocation should be consistent with industrial structural adjustment, which can save water by 9.8% in petroleum processing, coking coal and nuclear fuel processing, and 5.14% in chemical fiber manufacturing, which can be transferred to rubber and plastics sector. This paper presents suggestions on increasing regional ecological carrying capacity to realize high-quality development, establishing clean energy consuming system to raise energy efficiency, developing water-saving industries to materialize a coordinated sustainability in industrial development and water ecology.