A two-dimensional water quality model is established on a section in the middle reaches of Jinsha River, based on the numerical simulation method. Considering the situation within the reach of many sewage outlets, the transport of pollutants in the river is simulated. Calculation results reveal the distribution characteristics of pollutants concentration under the effect of multi-sewage outlet discharge. The results show that the transport of pollutants along the riverside has little effect on the other side of the river. According to the predicted results, the water quality of the water intakes near the downstream reaches may not meet the standard of water quality. Therefore, the water obtained by intakes is not suitable for irrigation. It is essential to carry out effective measures to improve the water intake scheme. The paper can provide a scientific basis for the planning and design of the reasonable water intakes of the Jinsha River.