Aiming at the problems of poor applicability of traditional header height detection mechanism, poor stability and large lag of automatic control system of combine harvesters, an automatic control system of header height of combine harvester was designed, which mainly included the profiling mechanism, controller, proportional valve, manual operation handle and display module. The profiling detection mechanism was composed of angle sensor, profiling plate, torsion spring and other structures. The key structural parameters of the profiling mechanism were determined by using the Adams simulation software and its working performance was verified. The gray prediction PID algorithm of header height was used to reduce the lag of the control model. The control system detected the height of the header from the ground through the profiling mechanism. After being processed by the controller, the height of the header was changed by adjusting the expansion of the header oil cylinder. The field test results showed that the working performance of the header automatic control system was stable. Under the working conditions of preset header height of 100mm and 200mm, the average deviation of the control system was within 21 mm, which met the real-time control demand of header height during normal operation of combine harvester. This research could provide intelligent design methods of combine harvesters.