In order to reveal the migration process of riverbed pollutants in the step-pool structure, and the relationship between the intensity of the hyporheic exchange and the single-wide flow and the height ratio, the appropriate step-pool pollution control engineering parameters are explored. Underwater flow simulation of steep-pool structures, the results show that the surface water enters the river bed upstream of the step ridge, driving out pollutants to the downstream river bed for discharge, and the clean area extends faster from the step ridge to the upstream. When it extends to the downstream asymptote, the migration speed of the pollutants slows down significantly. Under the conditions of riverbed gradient and flow, the intensity of the hyporheic exchange caused by the step-pool structure is about 37 times that of a flat riverbed. The intensity of the hyporheic exchange has a power function relationship with the single-wide flow and the height ratio. When the step-pool structure is artificially introduced, the step height is 0.4 m and the spacing is 30 m, the riverbed pollutant treatment works better.