The success rate of automatic transplanter seedling picking is affected by the harsh operating environment of the transplanter and the reduced output accuracy of the opening and closing positioning of the seedling-picking mechanism due to the interference of the external environment. To solve such problems, the paper proposes to use an adaptive fuzzy PID control algorithm as the opening and closing positioning-control system of the seedling-picking mechanism. Based on the theoretical analysis and calculation of the positioning accuracy of the seedling-picking mechanism, a mathematical model of stepper motor angular velocity control was established, and a stepper motor angular velocity control model based on fuzzy PID (conventional PID) control was established in MATLAB/Simulink. In order to further simulate the actual working condition of the seedling-picking mechanism, a simulation model of stepper motor control with disturbance was built, and the response results showed that the fuzzy PID control system could get rid of the disturbance faster under the action of external disturbance signals. The results of the opening and closing positioning test of the seedling-picking mechanism showed that the fuzzy PID control system has higher control accuracy and more stable control performance than the PID control system, which meets the design requirements.