This paper studies a two-layer control strategy for optimal operational control which is prevalent in industrial production. The upper layer determines and adjusts the target set values, while the lower layer makes the loop output track the target value. In the two-layer structure optimal setting control system, the widely used PID controller is used in the bottom layer. Firstly, the parameters of the PID controller are obtained by solving linear matrix inequalities (LMI). Secondly, for industrial processes with nonlinear harmonic disturbances, a disturbance observer is designed to estimate these disturbances. Thirdly, the effects of disturbances or noises are minimized by dynamically adjusting the setting points. This method does not change the structure or parameters of the bottom controller, and thus meets the actual industrial requirements to a certain extent. Finally, in the numerical simulation section, the value of the performance index before set-points adjustment is compared with that after set-points adjustment.