Abstract: The current harvesting of edible sunflowers can be discrete two-stage mode, including manual picking for the insert trays to dry for 7 to 10 days, and then machine picking, threshing and cleaning. Edible sunflower combine harvesting equipment is still lacking in adaptability, low cleaning loss, and impurity rate in the field, due to that mostly modified from wheat, and corn harvesters. Cleaning is one of the key steps in the mechanized harvesting of edible sunflower, which is directly related to the rate of impurity and loss of sunflower seeds. Sunflower cleaning device has been focused mainly on theoretical analysis and parameter optimization in recent years. However, only a single-hole sieve has been used to explore the seeds passing-through performance of various edible sunflowers, leading to a high impurity rate and large cleaning loss. It is a high demand for the low-loss and high-efficiency edible sunflower cleaning device, in order to promote the high mechanization level of edible sunflower harvesting. In this study, a new cleaning device was designed with the double-layer vibrating air-sieve for the edible sunflower, particularly for the low loss rate and impurity rate during mechanized harvesting. The device consisted of the fan, upper sieve body with guide tooth plate, lower sieve body of step shaking plate, and the drive mechanism of offset crank slider. The structural parameters of the edible sunflower cleaning device were then determined, where the sieve length was 1600 mm, the width was 900 mm, and the clearance of the upper and lower sieve was 120 mm. Mechanical design was also carried out to obtain the crank length of 32.5 mm, the slider stroke of 70 mm, and the slideway inclination of 23°. Two groups were determined by the upper and lower woven sieves with square hole diameters of 20, 18 mm, and 18, 16 mm, respectively. Two varieties of edible sunflower were selected as the ‘Sanrui No.10’ and ‘Sunflower 363’ with the threshing mixture of different seed sizes. The movement process of material on the sieve surface was analyzed to obtain the optimal working conditions and the influencing factors on the cleaning performance. The kinematics of the sunflower on the sieve was also explored to obtain the properties of seeds passing through the sieve using the Fluent-EDEM platform. The simulation results showed that the cleaning device with a vibrating air was successfully realized the cleaning work of sunflower seeds, indicating a reasonable structural design. Orthogonal tests were carried out on the self-developed shelf of the cleaning device, where the influence factors were the crank speed, airflow direction angle, and sieve inclination, whereas, the test indexes were the impurity rate and loss rate. The primary and secondary influencing factors were ranked in descending order of the crank speed, sieve inclination, and airflow direction angle. The optimal combination of parameters was the crank speed of 250 r/min, sieve inclination of 4°, and airflow direction angle of 21°. The optimization of parameter combination was repeated five times on the bench for validation tests. The results showed that the impurity rate of both varieties of edible sunflower was less than 3%, and the loss rate was less than 2%, fully meeting the standard for the mechanized harvesting of edible sunflower. The performance of the cleaning device was also better than before. This finding can provide theoretical support for the improvement and optimization of the cleaning system during mechanized harvesting of edible sunflowers.