In response to the poor cleaning effect of the brush-type soybean seeder, a lightweight mechanism of the brush-type soybean seeder was optimized and designed. We proposed a progressive seed-cleaning method. Firstly, mechanical analysis was conducted on the soybean seeding process to prevent excessive clearing of individual soybean seeds initially filled into the orifices by the seeding brush. A formula for expressing the force exerted by the seeding brush on stabilizing individual soybean seeds in the orifice was derived. Secondly, an analysis of the progressive seeding principle was performed, and theoretical calculations were carried out for the progressive seeding curves within the x-y plane and along the direction of the z-axis. The progressive seeding curves were determined. Factors affecting the seeding efficiency were analyzed, including the plate’s speed, the initial angle of the seeding brush, and the initial distance between the seeding brush and the seeding plate. Based on the Box–Behnken central composite design theory, using the seeding tray’s rotational speed, the initial angle of the seeding brush, and the initial distance between the seeding brush and the seeding tray as experimental factors, orthogonal experiments were conducted with the leakage rate and the over-cleaning rate as the indicators for the evaluation, and the working parameters were optimized. Validation experiments showed that with a plate speed of 29 rpm, an initial angle of the seeding brush of 54°, and an initial distance between the seeding brush and the seeding plate of 11 mm, the results were as follows: a skip-seeding rate of 1.23% and an over-seeding rate of 0.66%, indicating a significant improvement in seeding performance. A comparative experiment was conducted with non-progressive cleaning brushes, and the test results showed that the progressive cleaning brush reduced the leakage rate by more than 1% and the over-cleaning rate by more than 0.5%.