Existing fully-automatic transplanters suffer from issues such as low accuracy in conveying and positioning seedling trays, inefficient picking and throwing due to complex movement paths, and seedling damage during the picking process. To address these challenges, this study presents innovative devices for seedling conveying in the X-direction and seedling picking in the Y-direction, considering both row and longitudinal intervals, which simplifies the mechanical structure. Based on these devices, methods were developed to achieve precise seedling positioning in both X and Y directions using multi-sensor combinations and motor control. A Finite State Machine (FSM) model was employed to propose a cooperative method for conveying and picking seedlings, simplifying the execution order and enabling continuous action without dragging or injuring the remaining seedlings. Experimental validation using 72-hole trays demonstrated that positioning deviation increased with motor pulse frequency, with a maximum deviation of 1.35 mm at 800 Hz, which remains within operational requirements. The qualification rate of seedling positioning was 100 % under various transmission speeds. The soil damage ratio (sDR) was measured to evaluate picking success, revealing an average successful seedling extraction rate of 95 %. These research findings offer technical support for efficient coordination between seedling conveying and picking in automatic transplanters.