Desalination is a highly complex process, which requires an efficient and accurate control system in the plant to maintain operation at optimum conditions that result in energy savings and in preventing scale formation. A study of a multi-input multi-output (MIMO) control of mechanical vapour compression desalination systems is presented. A transient model was developed to describe the significant dynamics of a vapour compression desalination system. A dynamic model was simulated using the Matlab program to provide physical insight into the system's dynamic behavior. Two efficient PID controllers for both distillate and evaporation temperature were developed to attain good performance.