Soybean plants cultivated using mulched drip irrigation planting technology have the following characteristics during the harvest period: green stems and leaves, and a high straw/grain ratio. Moreover, the threshing device of a soybean combine harvester is difficult to adapt to, resulting in an increase in the accumulation and unevenness of the threshed mixture. This leads to an increase in impurity content and the loss rate. We conducted a single-factor experiment on a self-developed longitudinal/axial-flow soybean threshing and separation test bench, employing drum speed, feeding rate, and threshing clearance as experimental factors. The influence of the soybean threshing and separation device’s working parameters on the distribution and uniformity of the threshed mixture in the axial and radial directions of the drum was explored through experiments. The results showed that the mass of the threshed mixture and soybean seeds showed a trend of first rapidly increasing and then slowly decreasing in the axial direction of the drum. Additionally, the mass showed a distribution feature of large values on both sides and small values in the middle in the radial direction. A lower drum speed, greater threshing clearance, and a smaller feeding rate make the radial distribution of a threshed mixture more uniform. Based on the combination of the crushing rate and unthreshed rate, the optimal working parameter combination was determined to be as follows: a drum speed of 500 r/min, a feeding rate of 6 kg/s, and a threshing clearance of 25 mm. The findings of this research offer valuable insights for the structural optimization and design enhancement of threshing and cleaning mechanisms within soybean combine harvesters.