In order to meet the development demands of modern agricultural machinery automatic operation, the rice transplanter automatic operation system was designed to realize the automatic control of transplanting operation and driving speed. Taking the Iseki PZ-60 rice transplanter as the research platform, the automaticmanual integration control scheme with manual mode priority was designed for transplanting components and driving speed based on the controller area network (CAN) communication. Accordingly, the incremental proportional，integral and differential (PID) as well as expert PID algorithm were designed respectively aiming at the speed and transplanting control. Meanwhile, the combined control strategy for the autooperating transplanter was developed. Afterwards, the speed control effect of the proposed navigation control system was tested on the cement road and two kinds of paddy field each with flat bottom layer and uneven bottom layer respectively. The results showed that the average errors of speed control were 3.25%, 5.40% and 8.01%, respectively, the probability of the speed errors which was within 10% were 98.6%, 90.1% and 68.0%, respectively. A kind of paddy field with flat bottom layer was selected to conduct the combined control experiments. The results showed that the automatic combined operation control of the transplanter had approximately the same effect with that operated manually. The results indicated that the developed automatic operation system of the transplanter can meet the automatic operation requirements of the unmanned transplanter.