Aiming at the problems of difficult parameter tuning, poor anti-interference ability and low trajectory tracking accuracy of automatic weeding control systems in complex field operating environments, which lead to difficulties in mechanical seedling avoidance and weeding between soybean plants and a high seedling damage rate, a soybean inter-plant seedling avoidance and weeding control system optimized by (multi-strategyimproved whale optimization algorithm,MSWOA） is proposed. This system controls the angular velocity of the stepper motor to achieve precise seedling avoidance and weeding with the weeding knife. Firstly, a mathematical model for inter-plant seedling avoidance and weeding is established, and a fuzzy controller is combined with a linear active disturbance rejection controller (LADRC) to improve the anti-disturbance performance of the system. Secondly, the MSWOA is used to tune the key parameters of the fuzzy-linear active disturbance rejection controller (Fuzzy-LADRC). Comparative tests with benchmark functions prove that MSWOA has better optimization performance and stability. Finally, simulation experiments are conducted on the inter-plant weeding control system model to determine the optimal control method. The simulation results show that the improved algorithm-based control method exhibits faster convergence speed and higher convergence accuracy compared with other control methods, effectively enhancing the system′s control performance. Specifically, the Fuzzy-LADRC control system optimized by MSWOA reduces the disturbance recovery time by 86.0% and 10.9% respectively in contrast to the traditional PID and LADRC control systems. Additionally, by comparing the parameter tuning effects of MSWOA with other algorithms, the superiority of the improved algorithm in this control system is further verified. This control system possesses distinct advantages in antidisturbance capability and response speed, enabling it to adapt to complex field working environments and meet the control requirements for precise seedling avoidance and weeding operations.