Based on programmable controller PLC, a kind of control system that can pick up a row of tray seedlings and alternately cast tray seedlings was designed, it can be used for self-designed automatic transplanting machine and solving the problem of high precision and difficult coordination of the automatic transplanting machine. In order to reduce the inner damage of seedlings, the control system detects the status of picking process by three travel switches I1, I2 and I3 to make the picking seedling claws gradually stretching in inserting process. Using the photoelectric sensor to detect the position and quantity of seedling cups, and obtain its motion displacement by incremental encoder, therefore, the seedling pot was shot at the best casting place by their combination. Using 20 d cucumber seedlings in 72-holes and 128-holes seedling trays respectively, the experiments were conducted to test picking and casting performance of the control system. The results showed that if the planting frequency was between 40 and 70 plants per minute, the success rate of picking and casting was more than 95%, with average value of 97.98%. As the increase of planting frequency, the success rate dropped but changed a little, which proved that the autonomous designed control system can be used in different seedling trays and planting frequencies, achieving the goal of high-efficiency transplanting.