When harvesting forage seeds, the current harvester has high total loss rate and crushing rate, poor cleaning effect of impurities and insufficient settlement. In order to solve the above problems, theoretical and structural analysis on the basis of the existing settling box were carried out, the cleaning structure of the settling box in combination with specific requirements and the overall structure shape was improved, a circular arc decelerating baffle was designed, the impact force on the seeds was reduced, the size and position of the baffle were adjusted, and more seeds were made clean by settling. The qualified rate of forage seed harvest quality was improved. By means of computational fluid dynamics simulation, the internal flow field of the settlement separation unit was simulated. Reynolds stress model and DPM model were selected to simulate the gas phase and solid phase respectively to obtain the airflow field distribution diagram and the particle field motion trajectory diagram. The results showed that the circular arc deceleration baffle designed compared with the structure of the broken line deceleration baffle increased the seed settlement rate, reduced the seed crushing rate, and increased the bottom capture rate when the inlet wind speed was increased. Field experiments were carried out to harvest alfalfa by forage seed harvester, and the harvest qualification rates of baffle free and broken line reducer were compared. The results showed that the sedimentation loss rate was 0.19% and the crushing rate was 0.9%, both of which met the national standard and proved the effectiveness of the device.