Abstract: A threshing and separating device is one of the most important working parts of the combine harvester. The structural parameters of the threshing and separating device can also dominate the flow velocity distribution of the airflow field, even the cleaning quality of the combined harvester. However, the existing threshing and separation device has limited to adjust the distribution of the separated substances under different types and working parameters, resulting in a high crushing rate and loss rate. Particularly, it is still lacking the special soybean harvesters with the high threshing rate in Southern China. Therefore, the purpose of this study was to improve the distribution consistency of the airflow during threshing and cleaning. Four concave screens were designed to independently adjust the threshing clearance. The concave screen was driven by an electric cylinder to rotate around the hinge shaft. At the same time, a pressure sensor was also installed in the middle conveyor of the harvester. The threshing clearance was then switched to the automatic adjustment mode through the mobile phone. Meanwhile, the feeding amount and threshing clearance were calculated to detect the pressure of crops on the bottom of the intermediate device. As such, the automatic adjustment of threshing clearance was realized after adjustment. The optimal combination of parameters was also determined for the different crops. A threshing separation test bed was then constructed for threshing soybean, according to the threshing separation and cleaning device of the combine harvester commonly used in Southern China. Firstly, the velocity distribution of the airflow field was measured in the cleaning room. Then, the mass distribution of soybean, rice, and maize threshing was also measured at the symmetrical gap. The results show that the velocity of the airflow field was symmetrically distributed along the axis of the threshing cylinder. But the threshing velocity of three crops was high on one side and low on the other, or in the shape of a saddle. The threshing quality was also compared to the symmetrical and asymmetrical gap. The increasing gap on the side with the lower threshing quality then improved the total threshing quality. A similar trend was found in the above three crops. Finally, the quality of mechanized soybean harvest was further improved to optimize the parameters of the new threshing and separation device. The bench test and field verification show that the best quality of mechanical harvesting operation was achieved when the feeding rate was 3.4 kg/s, the length ratio of the front and rear cylinders was 1:2, the rotation speed of the front cylinder was 443 r/min, and the rotation speed difference of the cylinder was 93 r/min, while the left front threshing clearance was 22.7 mm, the front threshing clearance difference was 5.4 mm, the left rear threshing clearance was 18.6 mm, and the rear threshing clearance difference was 3 mm. The better performance was obtained under the optimal combination, where the mean crushing rate was 2.64%, the mean loss rate was 1.12%, and the mean impurity content was 1.97%. The asymmetric layout of threshing clearance improved the work quality better than the symmetrical layout. At the same time, the performance and verification tests were conducted on the optimal combination of parameters with corn and rice as test materials. The performance indexes were then enhanced during harvesting. The findings can also provide a strong reference to improve the adaptability of combine harvesters to different crops.