Deep eutectic solvents (DESs), as potential green solvents, can be used for the separation of the low-carbon alcohol azeotrope, which has become one of the hot spots in solvent research in recent years. In this work, choline chloride (ChCl)/glycerol (GI) (1:2) and ChCl/ethylene glycol (EG) (1:2) were used as extractants to study the extractive distillation process of isopropanol (IPA) dehydration. The high separation performance of the choline-based DESs was explained from the point of quantum chemistry. Economic impact, exergy loss, and environmental impact were compared between the new processes and the traditional process. The results displayed that the total cost of the two processes with DES as the extractant and using the heat pump process was reduced by 30.256, 30.918, and 36.229%, respectively. It saved a lot of cost and improved the thermodynamic efficiency. In terms of environmental impact, compared with the traditional process, the ChCl/GI (1:2) process reduced the emission of toxic and harmful substances by 39.94%, greatly improving environmental friendliness. The above results showed that the choline-based DESs performed excellently in the extractive distillation process for the separation of low-carbon alcohol azeotropes. Therefore, the development of new choline-based DESs is of great significance to the green, environmental protection and sustainable development of chemical and pharmaceutical industries.