The water resource system, related to society, economy and environment, is a compound feedback system. Supply and demand of the water resources in basins interacts with the development of social economy as well as the aquatic ecosystem. Therefore once suffering crisis of water shortage, not only the socioeconomic system will be confronted with large financial loss, but also the original aquatic ecological equilibrium in basins will be broken. This paper constructed an early warning system of water shortage by using Stella software based on the system dynamics (SD) model, which has been believed to delineate clearly the coupling correlation between the water resource and the social economic system and aquatic ecosystem. The ecological flow was considered as an indispensable element in the water demand. So the calculation model of ecological flow was involved in the SD model, which distinguished it from traditional model of water resources supply and demand. Moreover, the supply and demand ratio was chosen to predict the variation of supply and demand of the socioeconomic water as well as ecological flow by means of simulation under a given scenario of water shortage.