To address the inefficiency and instability of automatic transplanting machines, a dual-row seedling pick-up device and its corresponding control system were developed. Existing seedling end-effectors are primarily mechanically controlled, and the seedling needles can easily cause damage to the interior of the bowl. In order to reduce the damage inflicted by the end-effectors to the bowl, this paper conducted a mechanical analysis of the end-effector. At the same time, a buffer optimization analysis was conducted on the operation of the end-effector, and a flexible pneumatic end-effector for seedling picking was designed. The control system combined the detection of multiple sensors to monitor the process of seedling picking and throwing. By coordinating the lifting cylinder and clamping cylinder, the system effectively reduced seedling pot damage while improving seedling picking efficiency. By setting the operating parameters of the servo motor, the goal of low-speed and high-efficiency seedling picking was achieved. To evaluate the performance of the control system, the linear displacement sensors and acceleration testing systems were used to analyze the performance of the seedling throwing. The results showed that the seedling picking efficiency could reach 180 plants min−1, with no significant difference between the actual measured moving distance and the theoretical setting distance. The positioning error remained stable between 0.5 and 0.9 mm, which met the requirements for seedling picking accuracy. The buffer optimization design reduced the peak acceleration of the end-effector from −22.1 m/s2 to −13.4 m/s2, and the peak value was reduced by 39.4%, which proved the significant effectiveness of the buffer design. A performance test was conducted using 128-hole seed trays and 33-day-old cabbage seedlings for seedling picking and throwing. When the planting frequency reached 90 plants/row·min−1, the average success rate of picking and throwing seedlings was 97.3%. This indicates that the various components of the designed seedling pick-up device work in good coordination during operation, and the control system operates stably. Technical requirements for the automatic mechanical transplanting of tray seedlings were achieved, which can provide reference for research on automatic transplanting machines.