Aiming at the automatic control demands of the pneumatic ejecting type high-speed transplanter, an automatic control system for the transplanter was designed based on Arduino microcontroller. The system mainly included multi task modules of tray displacement detection, orderly tray supplying and high-speed seedling ejecting. Taking the position and displacement of the seedling tray as the main control conditions, the methods for controlling tray supplying speed and seedling ejecting interval were determined by analyzing the coordinated relationships of the tray supplying speed-tray feeding speed, and seedling ejecting interval-tray displacement. Two finite state machines were established respectively;the control flow was designed based on the dynamic time slice polling algorithm. The accuracy test of the control system was carried out to assess position accuracies, results of which showed that the maximum relative errors of tray supplying position and the seedling ejecting position were 1.27% and 12.85% respectively at high-speed (90~150 plants/min), the maximum cumulative relative errors of the 2nd to 6th seedling ejecting positions were 11.85%, 5.63%, 4.25%, 1.94% and 2.44%, respectively, which were all within the allowable error range and met the working requirements. The transplanting performance test was carried out with the indicators of the success rate of tray supplying, seedling ejecting and throwing. The test results showed that the automatic control system worked reliably at high-speed, the tray supplying and tray feeding motions were connected effectively, and the seedling ejecting sequences were synchronized with continuous tray feeding accurately, the success rate of tray supplying and the success rate of seedling ejecting were both 100%, and the success rate of seedling throwing was above 94.44%. The automatic working of the orderly tray supplying and seedling ejecting at high-speed of the pneumatic ejecting type high-speed transplanter was realized.