The cylinder length limits the threshing and separating ability of the horizontal axial flow threshing separation device, which is only used in the small and medium-sized combined harvesters. In order to study the effect of the cylinder speed, the feed rate and the concave clearance on the threshing performance of the horizontal flow threshing unit, a mathematical model was established to optimized its structure by using the probability theory. The verification tests were carried out, and the results showed that the average relative error of the prediction of the unthreshing rate is 8.23%, and the average relative error of the unseparated rate is 2.90%. Simulation analysis and single factor test showed that the model could reflect the influence of the threshing cylinder speed, the feed rate, the concave clearance and other parameters on the threshing separation performance.