In the process of vegetable plug seedling cultivation, packaging, and transportation, there may be missing, unhealthy or injured seedlings in the tray, which results in a missed planting or a low seedling survival rate after automatic transplanting. In this study, a seedling selection system with the function of seedlings identification, week seedlings elimination, and missing seedlings supplement was developed for an automatic transplanter. A plug seedling identification system based on a machine vision was used to detect vegetable plug seedlings based on the area characteristics of plug seedlings, stem leaves and plug bodies. The identification results were transmitted to a programmable logic controller (PLC), which controlled a nozzle to eliminate the unqualified seedlings from the conveyor belt lattice. When the empty conveyor belt lattice reaches the seedling throwing funnel, the rear conveyor belt lattice with the plug seedling is accelerated to ensure the continuity of seedlings supply. The adaptive fuzzy PID control algorithm was used to control the stepper motor of the conveyor belt to realize accurate seedling conveying and a seedling supplement. Using 30 days pepper plug seedlings as experimental seedlings, a comparative field experiment was carried out to evaluate the performance of the seedling selection system. The results showed that when the seedling selection system was turned on and the seedling extracting frequencies were 60, 80, and 100 plants/min, the success rates of plug seedling identification were 98.84%, 98.38%, and 96.99%, and the robust seedling rates were 98.05%, 97.78%, and 95.83%. The robust seedling rates were increased by 15.64%, 16.07%, and 13.89%, respectively, in contrast to turning off the seedling selection system.