Ratooning rice plants have a high moisture content and strong adhesion during harvesting. Traditional cleaning devices are prone to clogging when processing ratooning rice, resulting in a series of problems such as high grain loss rate and high grain impurity rate. In response to the above issues, this article adopts the CFD-DEM coupling method to design a spiral step cleaning device. A detailed analysis was conducted on the influence of the cone angle and thickness of the spiral-stepped skeletons on the flow state, and flow velocity and pressure distribution cloud maps were obtained under different structural parameters. The vortex morphology under different thicknesses of the spiral-stepped skeletons was compared, and the structural parameters of the device were determined. The motion trajectory and distribution of impurity particles under different inlet flow velocities were analyzed using data superposition, and the appropriate inlet flow velocity range was determined. A test bench was built, and a three-factor quadratic regression orthogonal rotation combination experiment was conducted with fan speed, feeding rate, and device inclination angle as experimental factors. The results of the bench test show that the performance index reaches its optimum when the device inclination angle, fan speed, and feeding rate are 2.47°, 2906 r/min, and 4.0 kg/s, respectively. At this time, the grain impurity rate, grain loss rate, and sieve clogging rate are 2.21%, 2.15%, and 3.5%, respectively. Compared to those of traditional cleaning equipment, these value are reduced by 44.5%, 39.6%, and 83.9%, respectively. This study can provide ideas for the design of ratooning rice cleaning devices.