In order to reduce the grain crushing rate and improve the cleanliness in the process of rice harvesting, three types of threshing elements, namely rod teeth, bow teeth, and cutter teeth, were designed based on the longitudinal axial flow differential segmented threshing drum. By changing the contact state between the surface of the threshing element and the grain during collision, six types of threshing rollers were obtained by rigid flexible coupling. Based on the impulse momentum theorem, the collision process between grains was analyzed. Through simulation experiments, it was found that the average normal force on grains was 28.4 N and 22.3 N, and the average tangential force on grains was 14.43 N and 8.74 N, respectively, when the rigid rod teeth and the rigid flexible coupling rod teeth came into contact with rice grains. Three-factor and three-level orthogonal test was carried out by taking the tooth shape of front roller, the rotation speed of the front roller and the rotation speed difference between the front and rear rollers as influencing factors, and the broken rate and undrained rate of rice as evaluation indexes. The test results show that the rotation speed difference between the front and rear rollers and the tooth shape of the front roller have the greatest influence on the broken rate and the un-threshing rate, respectively. The optimal combination obtained from the experiment is that the tooth shape of the front roller is bow tooth, the rotation speed of the front roller is 600 r/min, and the rotation speed difference between the front and rear rollers is 100 r/min. Compared with rigid threshing components, the average grain broken rate of rice can be reduced by 18.5%.