In order to solve the problems of halfway separating and high losing rate of the cyclone separation system, material movement analysis was done by using of highspeed photography. The wheat and mixture of stalk were chosen as the experiment objects, statistical experiment was carried out when diameter of air pores, rotating speed of the fan and rotating speed of the winnower were chosen as the experiment factors and cleaning rate and losing rate were chosen as the experiment indicators. Single factor experiment result showed that the arrangement of the air pores had effect on the cleaning ability. When the arrangement of the pores was spiral, the system performed better. The cleaning rate was increased first and went down later with the increasing of the rotating speed of the fan, winnower and the diameter of the air pores. The losing rate was increased with the increasing of the rotating speed of the fan, winnower and the diameter of the air pores, the value of losing rate was no more than 2%. Multifactor experiment result showed that when the rotating speed of the fan was 1900r/min, the rotating speed of the winnower was 1100r/min and the diameter of the air pores was 8mm, the cleaning system worked better, the average value of losing rate was less than 1.5%, which was reduced by 25% compared with the former.