A real-time, rapid emergency control (EC) model is proposed to cope with sudden water pollution accidents in long-distance water transfer projects. The EC model outputs the method of EC based on pollutant properties. A generalized form of EC model is proposed and tested with a demonstrative project. The rapid prediction formulas of emergency control parameters (ECPs) are proposed under different states of water diversion. The closing times of check gates and the pollution range are calculated by the rapid prediction formulas of ECPs. A case study is examined under the scenario of a sucrose spill in a demonstrative project conducted in the Fangshui to Puyang channel of the Beijing-Shijiazhuang Emergency Water Supply Project in the middle route of the South-to-North Water Transfer Project. The relative errors of peak concentration and arrival time of peak concentration are less than 20%. However, we could not use an actual toxic soluble pollutant to validate the EC model, so we performed the experiment with sucrose to test the EC model based on its concentration variation. The final result shows that the model is able to play a fundamental role in the decisions involved in the Emergency Environmental Decision Support System.