This paper explored the mechanism of dissociation of hemicellulose using lactic acid (LA)-based deep eutectic solvents (DESs) synthesized with different hydrogen bond acceptors (HBAs) via simulations. Density functional theory (DFT) calculations and molecular dynamics (MD) simulations revealed that DESs synthesized with guanidine hydrochloride (GuHCl) as hydrogen bond acceptor (HBA) demonstrated better hemicellulose solubilization compared to the conventional DESs synthesized using choline chloride (ChCl) as HBA. The best interaction with hemicellulose was achieved at GuHCl:LA = 1:1. The results showed that CL played a dominant role in the dissolution of hemicellulose by DESs. Unlike ChCl, the guanidine group in GuHCl had the delocalized π bond, which made CL have stronger coordination ability and promoted dissolution of hemicellulose by DESs. Moreover, multivariable analysis was employed to establish the correlation between the effects of different DESs on hemicellulose and the molecular simulation results. Additionally, the influence of different HBAs functional groups and carbon chain length on the solubilization of hemicellulose by DESs were analyzed.