In order to solve the problem existed in using of multilayer manure cleaning system carrying board which were manure accumulated at the end of multilayer manure, high demanding of large height of interlayer spacing in cage system, and poor stability of mechanical scraper, the discrete element analyses software EDEM 2.3 was used to numerically simulate the working process of multilayer manure cleaning system. The effects of the scraper vertical angle X1, the scraper longitudinal angle X2, and the inclination angle of manure carring board X3 on mechanical property of the multilayer manure cleaning scraper were analyzed. The reliability of the simulation model was verified by comparing the performance of virtual scraper and the multilayer manure cleaning scraper equipped in first generation prototype of 9LPT—3. Quadratic orthogonal rotation design with three factors was introduced by the simulation model, the width of manure deposit body after scraping process Y1, the maximum height of manure deposit body in scraping process Y2, and the stability of manure cleaning speed Y3 were selected as the indexes. The result showed that X1、X2 and X3 significantly correlated wih Y1 and Y2 (P<0.0001 and P<0.05 respectively), but didn’t correlate with Y3. It could be concluded that the most optimal mechanical property of the multilayer manure cleaning system would be obtained when x1、x2 and x3 were respectively selected as 7°, 35° and 5°.