An energy-saving complex distillation column, can separate ethyl acetate and isopropanol from pharmaceutical waste water. This allows reducing energy consumption and improve economically efficiency, was proposed by this article. According to the requirements of industrial carbon emission reduction, carbon tax and carbon emission rate, were added to the calculation of total annual cost (TAC). Based on Aspen Plus simulation, carbon emission reduction as a comprehensive optimization objective to optimize the process. The optimization results show that process is more energy-saving than traditional processes, the reboiler duty and TAC are respective reduced by 44.96% and 52.93%, and the carbon emission reduction is calculated accurately. This study provides the design and theoretical basis for the industrialization of similar organic matter separation process. [ABSTRACT FROM AUTHOR]