Aiming at the problem of low seedling picking success rate, high damage rate and poor stability of pepper transplanter, a kind of clamp-puncture end effector and pneumatic system was proposed based on the operation mode of taking seedlings in whole row and throwing seedlings at intervals. The structural configuration and working principle of device was analyzed and the kinematics and dynamic model was established. Based on the physical characteristics of pepper plug seedlings and analysis of boundary condition, the main parameters range of the newly improved end effector was determined. Simulation test based on ADAMS and FluidSIM-P 3.6 were carried out to verify the reasonability of the structure and response time sequence of pneumatic actuator. The coupling simulation test based on EDEM and RecurDyn turned out that the improved structure had a better performance. Aiming at the success rate of seedlings picking and the loss rate of substrate, single factor test and analysis were carried out on the key factors such as needle interval, needle insertion stroke and needle insertion angle. According to the results of single factor test, the orthogonal test, variance analysis and response surface analysis were carried out. The optimal parameters were obtained as follows: needle interval was 12.25mm, needle insertion angle was 50.37°, needle insertion stroke was 14.21mm, the seeding picking success rate, substrate loss rate were respectively 97.44% and 2.13%. Bench verification test showed that the success rate of seedling extraction was 97.92% and the matrix loss rate was 2.21%. The relative error between verification result and the predicted value was less than 5%.