Semi-conductor manufacturers in Taiwan often produce large amount of waste solution containing isopropyl alcohol (IPA) and water (H2O). In order to purify IPA, a simple pre-purification column is used first to purify the waste solution into the azeotropic composition of IPA and H2O. Then, an entrainer is added to further separate into high purity IPA product and waste water. In this work, control of an industrial scale complete heterogeneous azeotropic distillation column system of isopropyl alcohol (IPA) + water (H2O) with cyclohexane (CyH) as an entrainer is investigated. The complete system includes a heterogeneous azeotropic column, an additional recycle column, a decanter, and a recycle stream from the recycle column back to the azeotropic column. In early study of this system, the IPA product purity at the bottom of the azeotropic column is specified to be ultra pure with over 99.999 rnol% IPA. The temperature profile of the azeotropic column for this ultra pure separation is characterized by two temperature breaks inside the column. In this paper, the IPA product purity is relaxed to specify at 99.9 mol%. With this purity, the temperature profile and the route of the composition profile for the azeotropic column is completely different than the previous case. The suitable overall control strategy of this complete heterogeneous azeotropic distillation column system has been studied extensively in this paper. From process analysis and dynamic simulation, the overall control strategy is developed which requires reverse-paired two temperature loops in the first column and one temperature loop in the second column. The overall control strategy is tested with composition and flow rate variations in the fresh feed stream. The specifications of the IPA product and waste water stream with both purities at 99.9 mol% can be met despite various disturbance changes.