This paper proposes an overall solution to the two‐layer model predictive control (MPC) for the integrating controlled variables in the process model. The scheme includes three modules, that is, the open‐loop prediction module, the steady‐state target calculation (SSTC) module, and the dynamic control module. Based on the real‐time output measurements and past inputs, the open‐loop prediction module predicts the future outputs in the presence of disturbances. The economic optimization of SSTC is comprised of the feasibility stage and the economics stage, considering constraints of multi‐priority ranks. The dynamic control module receives the steady‐state targets from SSTC and calculates the control signals. The optimization problems of SSTC and dynamic control operate with the same frequency. This overall method guarantees the consistency of three modules with respect to the model, the constraints, and the targets. The simulation example illustrates that steady‐state targets are adjusted dynamically after the occurrence of disturbances, and offset‐free control is achieved.