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, according to the different components types of flax materials, the operation mode of “air cleaning first, and then air-screen separating” was put forward, the separation-cleaning technological process of flax threshing materials was developed, and a double duct system of air-screen separating and cleaning machine for flax threshing material was designed. Through design selection and parameter calculation of key operating components of the prototype, the important working parameters of the three stage vibrating screen, double duct impurities aggregate device and dust suction device were determined. The working conditions for the parameters of the crank connecting rod of the vibrating screen obtained with different components of flax material were in different motion states on three-stage screen surface. For the relevant work performance test of prototype, when the electromagnetic exciter amplitude of the vibration feeding system was controlled at 14~18mm, the front duct air volume control handle in 2~4 gear, the rear duct air volume control handle in 4~6 gear, the vibration frequency of three-stage vibrating screen was 2~6Hz, the operating machine had a strong adaptability to flax threshing material. After the operation of the double duct system of air-screen separating and cleaning machine for flax threshing material, the cleaning rate of grains was 97.16%, the entrained loss rate of was 1.12%, 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.