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In this work, CO₂ absorption capacities in a series of aqueous N-alkyl-N-methylmorpholinium-based ILs with acetate as the counterpart anion were investigated. Among these ILs, N-butyl-N-methylmorpholinium acetate ([Bmmorp][OAc]) with the highest CO₂ absorption capacity was screened for thermodynamic modeling. The non-random two-liquid model and the Redlich–Kwong equation of state (NRTL-RK model) were used to describe the phase equilibria. The CH₄ absorption capacity in the aqueous [Bmmorp][OAc] was also measured in order to verify the results predicted from the thermodynamic modeling, and the comparison shows the reliability of the model prediction. The parameters were embedded into the commercial software Aspen Plus. After that, the aqueous [Bmmorp][OAc] solutions with 30–40 wt % of water were selected to carry out process simulation for CO₂ separation from biogas, and it was found that using these aqueous [Bmmorp][OAc] gave rise to lower energy usage and smaller size of equipment than other physical solvents. The results suggest that aqueous [Bmmorp][OAc] solution can be used as an alternative to organic solvents and has the potential to decrease the cost of CO₂ separation.