Existing rape combine harvester has the challenges to separate the small rapeseed from the threshing outputs whose components are mixed, highlighting the need to improve the cleaning rate to reduce the labor consumption in manual re-cleaning process. Therefore, a modularized re-cleaning cylinder sieve, which could hung on the grain tank, was designed. Based on the kinematics and dynamic analysis, the range of structure and operation parameters of the material lifting screw conveyor and screening device were analyzed. A three-factor and three-level orthogonal experiment was carried out by using EDEM. The loss rate, cleaning rate and screening efficiency were taken as the indexes. The rotating speed of cylinder sieve, the screw pitch of the spiral blade, and the diameter of the sieve hole were taken as the factors. The optimal parameter combination was determined by the orthogonal experiment, and verified by the bench verification experiment. The simulation results indicated that the optimal parameter combination of the diameter of sieve hole, the rotating speed of cylinder sieve, and the screw pitch of the spiral blade were 5mm, 105r/min and 250mm, respectively. When the feeding rate was 0.6kg/s, under this condition, the loss rate, cleaning rate, and screening efficiency of re-cleaning cylinder sieve were 0.92%, 98.96% and 95.12%, respectively. The results of bench experiment showed that the cleaning system with re-cleaning cylinder sieve could work smoothly. Under the optimal parameter combination, the loss rate, cleaning rate, and screening efficiency were 0.96%, 98.67% and 95.36%, respectively. Compared with the performance of the cyclone separation cleaning device without re-cleaning cylinder sieve, the cleaning rate was improved by 4.38 percentage points. The research could provide a reference for the structural improvement and optimization of cleaning device of rape combine harvester.