Density functional theory (DFT), atoms in molecules (AIM) theory, natural bond orbital (NBO) analysis, and reduced density gradient (RDG) analysis were employed to investigate the mechanism of lignin dissolution in imidazolium-based ionic liquids (ILs). Lignin was modeled with guaiacyl glycerol-beta-guaiacyl ether (GG), which is one type of beta-O-4 linked dimers. Hydrogen bonds (H-bonds) are studied specifically and characterized by different methods to evaluate the strength of interaction between ILs and the lignin model compound. From the theoretical results, it is observed that H-bonds between anions and the GG model are stronger than those between cations and the GG model. Also, anions have the strongest interaction at the alpha-OH position of GG, while cations have the strongest interaction at the gamma-OH position of GG. In addition, anions Cl, OAc and MeSO4 have much stronger H-bonding ability than PF6, and the length of the alkyl chain does not have a significant influence on the cation-GG interaction. This work also simulates the interaction between the GG model and ion pairs, with the results suggesting that anions in ion pairs play a key role in forming H-bonds, and cations have a pi-stacking interaction with GG. The calculation data provide the interaction mechanism of lignin dissolution in ILs to some extent.