The problem of overexploitation and low efficient use of water resources in Nansihu basin has become the main factors which restrict the social economic development, while the water structure analysis is the precondition and foundation of water resources development and utilization. On the basis of Nansihu water structure analysis, the paper established the water structure SD model by Vensim software.The model took 2007 as the base year.Simulation time is from 2007 to 2025. The water structure change is simulated and predicted at conventional development mode. Through setting high, middle and low three speeds of economic development, the paper analyzed the impact of different economic development strategies on water structure. The results showed that the water use proportions of second industry and the tertiary industry are the highest in high program, while the water use proportions of second industry and the tertiary industry is minimum in low program. The change of water structure is affected mainly by the increase of water amount in second and tertiary industry. The simulation results can provide reference for the management of water resources and the establishment of economic development strategy in Nansihu and other watershed.