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, based on the study of the flow characteristics (accumulation angle and slip angle with steel of material) and separationcleaning technological process of flax threshing materials, a separating and cleaning machine for flax threshing material was designed. Through designing and selecting of key operating components of the prototype, the important working parameters of the vibration feeding system, grain separation device, suction fan and cyclone separator were determined. The operation process of automatic discharging discarded device was analyzed and the necessary work conditions to ensure automatic discharge were obtained. For the relevant work performance test of prototype, when the electromagnetic exciter amplitude of the vibration feeding system was controlled at 14~18mm, and the conversion frequency of the suction fan of the air cleaning system was controlled at 50~60Hz, the operating machine had a strong adaptability to flax threshing material. After the operation of separating and cleaning machine for flax threshing materials, the cleaning rate of grains was 9266%, the total entrained loss rate of was 158%, there was no obvious blockage in the automatic discharging discarded device and the experimental results met the design requirements of operation machine. The research results can provide an important reference for small grain crop threshing material separating and cleaning equipment development.