Separation process is very crucial in bioethanol production as it consumes the highest energy in the process. Unlike other works, this research systematically designed a suitable separation process for bioethanol production from corn stover by using thermodynamic insight. Two separation processes, i.e., extractive distillation (case 2) and pervaporation (case 3), were developed and compared with conventional molecular sieve (case 1). Process design and simulation were done by using Aspen Plus program. The process evaluation was done not only in terms of energy consumption and process economics but also in terms of environmental impacts. It was revealed that pervaporation is the best process in all aspects. Its energy consumption and carbon footprint are 60.8 and 68.34% lower than case 1, respectively. Its capital and production costs are also the lowest, 37.0 and 9.88% lower than case 1.