Abstract: Transplanting can be expected to reduce the growth period of crops for high land productivity, as well as mechanized operations. However, current vegetable transplanting still relies heavily on semi-automatic transplanters. Manual labor input is also required at present, compared with traditional planting. Furthermore, the complex movement trajectory of the seedling-picking mechanism can often lead to the relatively low efficiency of seedling picking. Hence, it is important to develop the seedling picking mechanism, in order to replace manual labor with high efficiency and strong adaptability. Fortunately, the non-circular gears can be expected to achieve the specific motion trajectories and the high-speed operation, due to their smooth transmission, compact structure, and long lifespan. This study aims to enhance the transmission efficiency and operational quality of the seedling picking in the automatic transmission mechanism for pepper plug seedlings. Some inspiration was also drawn from the successful applications of non-circular gear transmission mechanisms in high-speed rice seedling transplanting. According to the stem-clamping agronomic requirements of pepper plug seedlings, a 'slant clamping type straight pulling' stem-clamping was employed to simulate the manual seedling picking. The theoretical solution of the two-bar mechanism model was determined under the condition of one pose and one-rod length. Trajectory posture, speed control, and criteria were proposed to reverse design and control the posture and speed of each stage during seedling picking. A controllable posture and speed smooth 'fan-shaped' trajectory were obtained for seedling picking without recoiling or sharp edges. A continuous non-circular gear planetary gear mechanism was utilized to achieve the intermittent functions of low-speed seedling picking and steady-speed seedling planting. A mathematical model of the mechanism was established, according to the transmission characteristics and working principles of the non-circular gear planetary gear mechanism. A non-circular gear planetary gear mechanism-cam push rod mechanism was then designed for the stem-clamping seedling picking. Optimization analysis was conducted to clarify the impact of parameters (such as cam profile and gear ratio) on the mechanism using a Matlab-based analysis program. The optimization of mechanism parameters was validated for the high accuracy and rationality of component structural design. A physical prototype of the seedling-picking mechanism was then fabricated as well. A series of experiments were conducted on a test bench. Measurement and comparative analysis reveal that the actual working trajectory was consistent with the theoretical and simulated trajectories, indicating the high correctness of the mechanism design. Furthermore, experimental results also demonstrated the smooth and efficient transmission of the seedling picking mechanism. Specifically, the success rate of picking was 96.30% at a picking mechanism speed of 60 and 70 r/min. The success rate of planting decreased from 96.15% to 94.23%, with no seedling damage observed. At a picking speed of 90 r/min, the success rate of picking was 90.74%, the seedling damage rate was 1.85%, and the success rate of seedling throwing was 90.38%. The research findings can serve as a strong reference to develop the automatic seedling picking mechanism in the fully automatic transplanters for pepper plug seedlings.