Due to the special terrain of Chongqing City, various types of drainage trunks have been built along the Yangtze River and the Jialing River. Once a pipeline bursts, it will endanger the water quality of downstream water intake. Aiming at the establishment of a management system for sudden water pollution risk that may occur in the Chongqing Section of the Yangtze River after the impoundment of the Three Gorges Reservoir up to 175 m, a two-dimensional hydrodynamic water quality coupling model was built based on the measured topographic and hydrological data, and optimal inversion method was used to determine the roughness. The finite element method was applied to simulating the temporal and spatial variations of pollutant concentrations including the five-day biochemical oxygen demand (BOD₅), the chemical oxygen demand (COD), the total nitrogen (TN), and the total phosphorus (TP) under the condition that the fractured pipeline be completely repaired after 24 h or 48 h in the high and low water periods. The simulation results can provide a scientific basis for the optimization of the emergency plan in case of a sudden drain pipe rupture in Chongqing.