In order to improve efficiency, quality and resource utilization in continuous industrial production processes, an optimal operational control method with a two-layer structure was proposed for a nonlinear systems with input saturation. At the bottom of the two-layer structure, that was, the loop control layer, the convex hull representation method was used to deal with saturated nonlinearity and a PI controller was designed to ensure the system's tracking performance of the target value. In the upper operating control layer, the disturbance to the system was estimated through the disturbance observer, and on this basis, an algorithm for dynamically adjusting the set value was designed to suppress the disturbance, therefore optimizing the system control performance so that the system output can still be track setpoints. Finally, the effectiveness of the proposed method was verified through numerical simulation, the output of the system can be effectively tracked to the set points under disturbance.