Under the restriction of water resources，how to adjust the industrial structure is the scientific question for regional social and economic development. Taking the greatest GDP and the least water quantity as object function, the paper constructed the input-output model of water resources dynamic. With the input-output balance, economy, the total amount of water resources constraint, and the introduce of investment coefficient as the dynamic basis, the paper investigated the relationship between water and industrial structure. On the basis of analyzing the situation of water resources and problems, by use of optimization model of the multi-objective dynamic input-output constructed by the water resources input-output table of Jiangsu Province in 2010,the paper calculated the economic output value of every department in Jiangsu Province from 2011 to 2015 by MATLAB optimization algorithm. Through analyzing the relationship between output and Million yuan output value of water consumption,the paper calculated the water quantity of every department. The result can supply quantitative data for economy development and exploiration of water resources in the future in Jiangsu province, and provide support for the most strict management system of water resources in Jiangsu province.