An automatic control system for on-line rail heat treating unit, which suits Chinese production situation, is introduced. The system adopted continuous rail entering way. The coolants are "water-air mixture" or "wind". The cooling process was controlled in segments. Roller bed velocity and fan were controlled with variable voltage variable frequency device. Heat treating time, wind-cooling intensity and nozzle displacement could be controlled automatically. The function of detection and processing for associated process parameters was provided also. Industrial test and batch production result show that the control system worked properly, the mechanical and wear resistance properties of the heat-treated rail were stable and met the project's requirements. The system had achieved its anticipated objectives.