In view of the problem that removing abnormal plants in breeding rape requires a large amount of labor and is inefficient, combined with the planting requirements of breeding rape, a shovel-tooth end-effector was designed, and a shovel-tooth removal test bench was built. A simulation model based on MBD (Multibody Dynamics)-DEM (Discrete Element Method) coupling was constructed. Then we conducted a Box-Behnken test with four factors and three levels. Taking the angle of soil penetration, speed of soil penetration, depth of soil penetration and speed of shovel-tooth gathering as the test factors, the soil penetration force and shovel-tooth gathering force as the test indicators. The mathematical regression model between test indicators and test factor was established. After optimizing the parameters of the model, the best combination of parameters with low soil penetration force and low shovel-tooth gathering force was obtained: angle of soil penetration of 84°, speed of soil penetration of 9 cm/s, depth of soil penetration of 8cm, and speed of shovel-tooth gathering of 6 cm/s. The simulation model was validated by field experiments. The average soil penetration force and average shovel-tooth gathering force of the three groups of pull-out tests were 34.8 N and 763.0 N, respectively. The removal rates were 96%, 92%, and 94%, all greater than 90%, indicating that the removal effect of the shovel-tooth end-effector was good, and the parameters were reasonably designed. The results can serve as reference for the design of rape abnormal plants removal device and the operation of MBD-DEM coupling simulation end-effector.