In order to solve the technical problems of high rate of breaking and un-threshing in the threshing process of cabbage seeds, based on the conventional spike teeth- grid concave threshing unit, a low damage threshing unit with the combination of flexible spike teeth with round heads and a concave with circular tubes was designed. In this study, Hertz contact and collision theory was used to analyze and determine the structural parameters of the new threshing unit. The interaction force of different threshing elements, concave and materials were analyzed by using discrete element method. The feasibility of the flexible threshing unit was verified by the comparison test of the distribution of threshed mixture. Finally, in the orthogonal experiment, the rotating speed of the cylinder, the concave clearance and the feeding rate were taken as the experimental factors, and the breaking rate and the un-threshing rate of the Chinese cabbage seeds were taken as the experimental indexes, the optimal working parameter combination of the threshing unit was obtained by using the weight matrix method. Under the condition the rotating speed of the threshing cylinder 750 rpm, the concave clearance 20 mm, and the feeding rate 1.4 kg/s, the threshing performance of the flexible threshing unit was the best. At this time, the breaking rate was 0.064%, and the un-threshing rate was 0.67%, which both met the relevant industry standards.