Choline-amino acid based ionic liquids ([Cho][AA]) have emerged as a significant class of biocompatible ionic liquids with promising applications in CO2 capture. This research investigates the interactions and structural properties of four specific systems: [Cho][Gly], [Cho][Ala], [Cho][Ser], and [Cho][Pro], utilizing density functional theory (DFT) and molecular dynamics (MD) simulations. Quantum mechanical studies suggest two distinct mechanisms for chemisorption, revealing a trend in energy values that decreases with the increasing size of the amino acid side chain: [Cho][Gly] < [Cho][Ala] < [Cho][Ser] < [Cho][Pro]. Calculations combined with noncovalent interactions studies unveil the mechanisms that favor the ammonium-carbamate with respect to the carbamic acid one, correlating with experimental insights. The MD simulations elucidate the cation–anion interactions, with radial distribution function (RDF) analysis indicating significant variations across different ionic liquid environments. Strong interactions are noted in [Cho][Ala] and [Cho][Gly], whereas [Cho][Pro] exhibits the weakest interactions. Additionally, the introduction of dimethyl sulfoxide (DMSO) effectively reduce the density during CO2 absorption processes, thereby enhancing fluid dynamics and promoting more efficient CO2 capture. These findings highlight the potential applications of these ILs in solvent extraction and carbon capture technologies. This study establishes a foundation for future research to optimize choline-based ILs for practical applications in environmental and industrial contexts, emphasizing their role as promising agents for CO2 separation.