Aiming at the problems of low success rate of seedling taking by the existing end-effector and easy to hurt the seedlings in the transplanting and seedling taking process, a seedling picking device was designed based on Ⅱtype geared five bar mechanism. The kinematic model of the seedling picking device was established, the working trajectory and position of the seedling picking device were optimized, and the main factors affecting the damage degree of the pot seedling were analyzed. Taking chili pepper pot seedling as the research object, the coupled mechanical-pot seedling model was established through EDEM-RecurDyn co-simulation to simulate and analyze the seedling picking process, and the simulation single-factor experiment was carried out with the insertion depth, seedling picking claw turning angle, and seedling picking angle as the test factors. The magnitude of the compression force exerted on the substrate and the number of Bond keys between the substrate particle over time were analyzed at different levels of factors during the seedling pickup simulation process. A three-factor, three-level orthogonal experiment was conducted by setting up a prototype machine to test the success rate of seedling pickup and the loss rate of pot quality. At the best parameter combination of insertion depth of 25mm, seedling picking claw turning angle of 4°, and seedling picking angle of 0°, a validation test was carried out with 128 cells of chili pepper seedlings, and the success rate of seedling picking was 93.33%, and the rate of substrate loss was 1.56%.