In order to solve the problems of soybean grain mixing and mechanical damage caused by single threshing process of soybean. A threshing device was designed for singleplant thresher with differential speed flexible belts. Single threshing was an important part of breeding experiments because it can avoid mixed seeds when there was smaller breeding area, small sample size and precious varieties. Meanwhile, most of the existing threshing devices were rollertype and made by rigid materials, which could cause mechanical damage to the soybean grains easily. However, the new soybean threshing device solved the problem of mechanical damage which would affect the germination and emergence of soybean seeds. And in order to find the optimal combination of the structure and working parameters of the differential flexible belt type soybean thresher, the method of fourfactor with fivelevel quadratic regression orthogonal rotation center combination was employed. The factor of cylinder clearance, top and low section velocity difference, low section velocity, threshing trip were discussed. And the loss of unthreshed grain, loss of entrap grain, cracked grains and average productivity were selected as evaluating indexes. The results showed that the rank of the effect of four factors on loss of unthreshed grain from high to low was as follows: top and low section velocity difference, the cylinder clearance, low section velocity and threshing trip; on loss of entrap grain: low section velocity, the cylinder clearance, threshing trip, top and low section velocity difference; on cracked grains: the cylinder clearance, top and low section velocity difference, threshing trip and low section velocity; on average productivity: threshing trip, low section velocity difference, the cylinder clearance, top and low section velocity difference. In the case of soybean grain with 16%~18% moisture content, the optimum combination region of the 〖JP2〗cylinder clearance was 7.55~13.00mm, the top and low section velocity difference was 0.59~0.70m/s,〖JP〗 the low section velocity difference was 0.84m/s, the threshing trip was 660mm; under this condition, loss of unthreshed grain was less than 12%, loss of entrap grain was less than 09%, cracked grains were less than 0.8%, average productivity was more than 35kg/h. The results laid a theoretical foundation for the development of singleplant thresher with differential speed flexible belts.