Targeting the problems of low precision and heavy workload in conventional screening of filled and unfilled grain in single-plant rice testing, a screening system for filled and unfilled grain was designed based on the coupling of the wind and gravity fields. In this study, the motion state of filled and unfilled grain in the flow field and the results of screening were analyzed and combined with aerodynamics. In order to reveal the influence law of the structural and working parameters of the screening system on the screening performance and determine the optimal parameter combination, this study conducted a quadratic regression orthogonal rotating center combination test with four factors and three levels based on the DEM–CFD coupling method. The relationship between air inlet wind speed, air cross-section shape, horizontal distance, vertical distance, and removal rate was studied. The results showed that, in a certain range, the removal rate was positively correlated with the section width of the outlet, positively correlated with the wind speed, and negatively correlated with the vertical distance and horizontal distance of the seed-drop outlet. The optimization results showed that, when the section width of the outlet was 75.44 mm, the wind speed was 8.90 m·s−1, the transverse distance was 198.78 mm, and, when the vertical distance was 34.87 mm, the screening rate of the screening system could reach 99.6%.