Decision support system (DSS) is a flexible information technology system that is useful in making semi-structure and non-structure decisions. This paper takes Toutun river basin in Xinjiang as a typical study region, combines "3S"(RS, GIS, GPS), digital 3D virtual emulation and seamless integration of multi-source spatial data with hydrological basin model, forecasting model, reservoir regulating model and damage estimation model to create a DSS for flood prevention. With this DSS, some difficult issues concerning flood prevention are explored. The characteristics of the DSS for flood prevention for this river basin include: decisions are made spatially-distributed, real time, mutual and by group. The DSS is a software platform with diversity and expandability. It contains intelligent and visualization functions.