Due to the existing problems of high loss rate and impurity rate when corn grains are directly harvested by the cleaning device of vertical flow threshing device with high feed volume, a double-layer vibration system with compact structure, strong cleaning ability, good cleaning effect and high reliability was designed. A double-layered independent vibrating cleaning method of corn grain was proposed. The movement law of screen surface and material was determined through analysis, the structural parameters of cleaning screen and double air duct and motion parameters of the transmission mechanism were obtained. Based on three evaluation indicators of the grain impurity rate, grain loss rate and distribution ratio, single-factor tests were conducted on the crank speed to determine the best operating parameters with upper and lower crank speeds of 220r/min and 190r/min, respectively. With two factors of crank length of upper and lower screen and three levels of 40mm, 45mm and 50mm, the orthogonal test was carried out to acquire the optimal cleaning results that the crank lengths of upper and lower screen were 50mm and 40mm, respectively. Finally, under the above experimental conditions, the results showed that the grain loss rate, grain impurity ratio and grain distribution ratio were 0.45%, 0.76% and 1.92%, respectively, when the feed rate was 8kg/s, and the cleaning effect of the device was better, which can meet the cleaning performance requirements.