Deep eutectic solvents (DESs) have great potential for desulfurization/denitrification of oil. This work investigated the underlying effect of hydrogen bond acceptors (HBAs) in DESs on the extractive removal of quinoline, carbazole and dibenzothiophene (DBT) from oil on the basis of the intermolecular interactions. With the acid-base interaction, quinoline was almost completely removed (∼100 wt%) in the acidic DES solvents. Differently, the hydrogen-bonding interactions enable the effective removal of near-neutral carbazole (96.0 wt%) and DBT (92.6 wt%) with assistance of H2O2. The partial addition of metal chlorides as the HBAs could further increase the desulfurization efficiencies to 94.7 wt% in 40 min due to the coordination-bonding interactions. Density functional theory (DFT) results confirmed that the HBAs are capable of regulating the interactions between heteroatomic compounds (e.g., carbazole) and DES components by manipulating the intrinsic hydrogen-bonding interactions in DESs, which further determines the desulfurization/denitrification performance. For the purification of catalytic diesel, the H2O2-assisted desulfurization and denitrification efficiencies were 60.0–69.0 % and 62.0–65.0 %, respectively. The intermolecular interaction analysis examined here provides guidance to improve the desulfurization/denitrification efficiencies in green DES extractants.