Benzyltriethylammonium chloride (BTEAC)-based deep eutectic solvent (DES) has a high delignification rate in the pretreatment of lignocellulose, and the lignin obtained from the removal has the advantages of high purity and low molecular weight. The interaction mechanism between BTEAC-based DES and lignin at molecular level was investigated by multiscale simulation analytical approach. By analyzing the types of weak interaction, charge distribution, number of hydrogen bonds, energy distribution and density distribution in different systems, the influence of six hydrogen bond donor (HBD) structures on the extraction process was clarified. The interaction between Cl- and lignin is mainly electrostatic interaction, and the interaction between BTEA+ and lignin is mainly van der Waals (vdW) interaction. The original π-π stacking of lignin is replaced by the new π-π stacking between BTEA+ and lignin. The effects of different functional groups and length of carbon chain on the interaction were researched. The acidic HBD with short carbon chain has a larger interaction and can affect the ether bond on the lignin. Among them, due to the smaller volume of formic acid (FA), it provides more space for BTEA+ to contact with lignin, resulting in stronger interaction. The molecular-level theoretical foundation underpinning the efficacy of BTEAC-FA in lignin removal during the pretreatment process is provided.