Water pollution accidents occur in drinking water sources may pollute water environment, destroy water ecological balance, and threaten the drinking water safety for residents. Based on water quality hydrodynamic mathematical equations and Digital Elevation Model, a new water pollution accident prediction program for drinking water sources in Three Gorges Reservoir under different hydrological conditions was developed. Moreover, this new program was firstly used to forecast and analyze flow field changes and concentration reduction of a hazardous chemical pollution accident in Huangjuedu drinking water source. By comparing the calculated values and the measured ones of February 10 to February 19, 2016, the maximum relative error was less than 10%, which indicated that the new program was feasible and reasonable. For pollution accident prediction in the drinking water source, the results showed that the maximum transverse velocity had stabilized as 2.070 m/s, 2.411 m/s and 2.717 m/s since 20 min after the accident responding to discharge flow of Xiangjiaba with 1800 m3/s, 2700 m3/s,and 3600 m3/s, respectively. The maximum vertical one was 1.372 m/s, 1.598 m/s and 1.872 m/s respectively since 20 min after accident under the corresponding conditions. Furthermore, the water quality of the drinking water source met the standard 23 min after the accident under the condition that the discharge flow of Xiangjiaba was 1800 m3/s. For conditions that discharge flows were 2700 m3/s and 3600 m3/s, the corresponding times to meet the standard were 21 min and 20 min after the accident, respectively. Thence, relatively large dispatch flows would help reduce the impacts of pollution accidents and accelerate water quality improvement of drinking water sources. This study provides a new and useful tool for predicting the diffusion and migration of pollutants in drinking water sources of Three Gorges Reservoir. And it also gives a practical reference for decision makers to forcast hazardous chemical pollution accidents in drinking water sources.