A tray tower was designed to verify the absorption performance of CO2 in 1-butyl-3-methylimidazolium glycinate ([Bmim][Gly]), 1-butyl-3-methylimidazolium lysinate ([Bmim][Lys]) and tetramethylammonium glycinate ([N1111][Gly]) activated MDEA (N-methyldiethanolamine) aqueous solutions. The simulated flue gas was composed of 15% (mole fraction) CO2 and 85% N2 and the experiments were performed at 313.2 K. To find a suitable absorbent composition, the mass fractions of MDEA and amino acid ionic liquids (AAILs) respectively ranged from 0.200 to 0.400 and 0.025 to 0.100. The removal efficiency of CO2 (ηCO2) and the overall volumetric mass transfer coefficient (KGav) were determined. The effects of absorbent composition (w), absorbent flow rate (L), gas flow rate (G) and plate number (Np) on ηCO2 and KGav were demonstrated. Our results showed that, when activated by AAILs, MDEA aqueous solution was able to absorb CO2 in tray tower efficiently, and both ηCO2 and KGav were significantly increased, e.g., in the case of wMDEA = 0.200, ηCO2 and KGav were increased from 43.48% to 95.55% and from 0.0069 (kmol m−3 h−1·kPa−1) to 0.0350 (kmol m−3 h−1·kPa−1), respectively, when w[N1111][Gly] was changed from 0 to 0.100, indicating AAILs activated MDEA aqueous solution is of great potential for industrial application in CO2 capture process.