Flax is one of the important oil crops in Northwest China, and Gansu Province is one of the main producing areas of flax. To enhance the mechanization level of separating and cleaning of flax threshing materials, a separating and cleaning machine for flax threshing material was designed. For further study of the improved working performance of separating and cleaning machine for flax threshing material, the single factor parameters obtained with the analysis were determined by numerical simulation test, the Box-Behnken experimental design with three factors and three levels was performed, parameters such as amplitude of feeding device, adjust thickness of material layer and rotate speed of impurity suction fan were selected as independent variables, which would influence the seed impurity rate and the cleaning loss rate. The mathematical model was established, and then the effects of various parameters and their interactions were analyzed as well. The test results showed that effects orders of three parameters on the seed impurity rate from primary to secondary were as follows: rotate speed of impurity suction fan, amplitude of feeding device and adjust thickness of material layer. And effects orders of three parameters on the cleaning loss rate from primary to secondary were as follows: rotate speed of impurity suction fan, adjust thickness of material layer and amplitude of feeding device. The optimal working parameters were amplitude of feeding device of 16.5mm, adjust thickness of material layer of 7.0mm and rotate speed of impurity suction fan of 1775r/min (that was, the speed conversion frequency of the impurity suction fan was 59.2Hz). Confirmatory tests showed that the average value of the seed impurity rate and the cleaning loss rate were 7.86% and 1.58%, which compared with before the optimization had dropped significantly, the degree of impurity and loss of flax threshing material in mechanized separation and cleaning could be alleviated under the condition of optimizing working parameters. The results can provide theoretical basis and technical references for the parameter selection and optimization of small grain crop threshing material separating and cleaning equipment development.