Ionic liquids (ILs) show good performances in SO2 separation science, e.g., SO2 capture from high-temperature flue gas or separation from gas mixtures. In this work, the mechanism of capturing SO2 by three guanidinium-based ILs, 1,1,3,3-tetramethylguanidinium lactate ([tmgHH] [L]), 1,1,3,3tetramethylguanidinium bis(trifluoromethylsulfonyl)imide ([tmgHH] [Tf2N]), and 1,1,3,3-tetramethylguanidinium tetrafluoroborate ([tmgHH][BF4]), is investigated by using molecular dynamic simulation and ab initio calculation. The results of condensed phase molecular dynamic simulation for the mixtures of SO2 and these three Its indicate the similar SO2 organization and interaction among them; SO2 may organize around [tmgHH](+) while it favorably organizes around the anions through Lewis acid-base interaction. Gas phase ab initio calculations show that [tmgHH][L] chemically interacts with SO2 while [tmgHH] [Tf2N] and [tmgHH] [BF4] do not, which is supported by the earlier FT-IR and H-1 NMR. data and is also consistent with the experimental result of a much higher absorption capability of [tmgHH] [L] for SO2 than the latter two. The anion plays a key role in the chemical interaction between [tmgHH][L] and SO2, the S atom is bonded to the N atom on-NH2 of [tmgHH](+), and some products with aminosulfate or aminosulfinic acid fragment may be formed. This work shows that IL structures should be carefully tailored for their final application in SO2 capture.