An automatic tuning control system and method for controlling air pollution control systems such as a dry flue gas desulfurization system is described. The automatic tuning control system includes one or more PID controls and one or more supervisory MPC controller layers. The supervisory MPC controller layers are operable for control of an air pollution control system and operable for automatic tuning of the air pollution control systems using particle swarm optimization through simulation using one or more dynamic models, and through control system tuning of each of the PID controls, MPC controller layers and an integrated MPC/PID control design.