In order to study the mixing rule of pollutant at a flow confluence of open channel, a 90° open-channel confluence of equal width was chosen as the study area. A three-dimensional hydrodynamic-pollutant coupling transport mathematical model was established and validated. The simulation was performed for six cases of different flux ratios. The results indicate that, the distribution of pollutant at the flow confluence shows obvious three-dimensional characteristics, which is closely related to the secondary flow. The relation between the maximum width of the polluted zone and the flux ratio on the surface of water is different from that in the interior of water body. The maximum width of the polluted zone of the water surface is equal to the width of main channel under low flux ratio cases and does not change with the flux ratios. However,it presents a good linear function relation with the flux ratio under high flux ratio cases. The relation between the maximum width of the polluted zone and flux ratio is quadratic in the middle and bottom water. The mixing of pollutant is less uniform if the flux ratio is closer to 0. 5. The mixing rate of pollutant is faster if the flux ratio is higher.