To improve the operating quality of the micro rice-wheat combine harvester in hilly and mountainous areas, an air-flowing cleaning unit was designed. By means of design and calculation, the main working parts’(cleaning unit, suction tube and suction fan) structure parameters and working parameters were defined. Simulating analyses on 3D model of air-flowing field in the cleaning unit were done. The results showed that the cleaning device structure and distribution of air-flow speed met the design requirements well and the cleaning effect was good. The compared field test with the rice harvest showed that the micro combine harvester with air-flowing cleaning unit had the features of compact size and easy operation. The distribution of air-flowing velocity and pressure in the cleaning unit could meet design requirements well. Comparing to micro combine harvester without air-flowing cleaning unit, the total loss rate decreased from 3.8% to 2.34%, the damage rate decreased from 1.5% to 1.4% and the impurities rate decreased from 7.2% to 1.2%, which fell by 38.42%, 8.33% and 8333%, respectively. Every performance reached the demands to JB/T 5117—2006 well. The decline of impurities rate was particularly significant.