Various solvents have been proposed considering the importance of CO2 gas removal from the environment. Over the past few decades, ionic liquids (ILs) have elicited much attention due to their unique properties. In this regard, capturing the CO2 gas by phosphonium-based amino acid ILs (AAILs) was studied by molecular dynamics (MD) simulation. The effect of cation functionalization was studied. The anion was glycinate, [GLY]-, and the cation was tetrabutylphosphonium, [P4444]+, functionalized by different functional groups including acidic (−COOH), alcoholic (−OH), amine (−ΝΗ2), and ether (−OCH3). Density, absorption energy, radial distribution function (RDF), mean square displacement (MSD), concentration profile, free volume, and fractional free volume were under investigation. According to density values calculated from MD simulation, functionalized AAIL with a carboxylic acid group ([P4444COOH][Gly]) is the most concentrated system with the maximum interaction energy between AAIL and the trapped CO2 gas equal to − 1.917 kcal.mol−1. In addition, the lowest volume variation was observed through this physical absorption. RDF analysis reveals that anion interaction with CO2 gas is the most considerable one in the case of [P4444COOH][Gly] AAIL. The CO2 uptake is 2:1 for functionalized AAILs that shows cation functionalization improves CO2 gas absorption capacity; each mole of [P4444COOH][Gly] AAIL is capable of surrounding 2.11 mol of CO2. Finally, the gas diffusion coefficient is the lowest one in [P4444COOH][Gly] AAIL as the solvent-free volume is observed as a continuous channel to trap CO2 gas with the lowest gas diffusivity parameter.