This paper briefly introduces a theoretical calculation procedure for modeling and simulation of a distillation process based on the energy balance method. The mathematical modeling is developed over three steps: the basic nonlinear model, the full-order linearized model and the reduced-order linear model. A modified MPC controller for ill-conditioned process with output regions is developed to improve the robustness of the controller. Compared with the traditional method, the modified method with output regions proves its superiority because it still maintains penalty on the output deviation from the desired region into its controlled objective function.