Existing cyclone separation cleaning device, which uses the suspending airflow to separate rapeseed from the threshing outputs, still has the challenge to improve the performance, highlighting a need to reduce the airflow inside the cyclone separator for rapeseed combine harvest. As a solution, cyclone separation cleaning device with raised cylinder disturbing airflow field was put forward. The internal airflow field would be disturbed by raised cylinders that were spiral arranged in the inner wall of the lower cone of the cyclone separator. The effect of airflow dead zone on the migration of rapeseed was studied based on dynamics and kinematics analysis, and the kinematical equation indicated that the dead zone would not benefit the performance of the cleaning device. Besides, the arrangement of the raised cylinders was clarified. By taking the inlet and outlet velocities, spiral angle, space, and spiral number of the raised cylinders as the factor, while the cleaning ratio and loss ratio were considered to be the evaluation indexes, the single factor experiment and Box-Behnken experiments were carried out based on the self-developed test-bench for key components of rapeseed combine harvester. Furthermore, the mathematical model of the relationship between cleaning ratio, loss ratio and the factors were established to figure out the optimal parameter combination of the cleaning device. The single factor experiment results illustrated that the raised cylinders could help improve the performance of the cleaning device. The loss ratio was low and the cleaning ratio was relatively higher when the number of spirals was 4. Box-Behnken experiment results showed that the optimal parameter combination were the spiral angle of 66.2°, space between raised cylinders of 48.3mm, inlet velocity of 4.9m/s, and outlet velocity of 25.4m/s. Under the optimal condition, the predicted values of cleaning ratio and loss ratio were 94.71% and 3.58%, respectively. Meanwhile, the measured values of cleaning rate and loss rate, obtained by bench test, were 93.87% and 4.21%, respectively. The field experiment showed that the cyclone separation cleaning device operated smoothly in the field, and the cleaning ratio and loss ratio were 90.03%~92.78% and 4.52%~5.07%, respectively. The research result could provide a reference for the structural optimization and improvement of the cleaning device for the rapeseed combine harvester.