Choline chloride-based deep eutectic solvents (DES) have been demonstrated as promising green solvents for the extraction of flavonoids and polyphenols. This study investigates the interaction between six different hydrogen bond donors (HBD) choline chloride-based DES and three types of polyphenolic flavonoid substrates. Density functional theory (DFT) and molecular dynamics (MD) simulations suggest that Cl− dominates the interaction primarily through electrostatic forces. The extraction effect of alcohol DES on rutin was optimized obviously, and the maximum interaction could reach 737.6 kJ/mol. Acid DES has a better extraction effect on anthocyanins, with a maximum interaction of 376.4 kJ/mol. With the increase of the carbon chain of HBA and the increase of the number of functional groups, the interaction between DES and the active substance decreases. As HBD, ethanolamine with both hydroxyl and amino groups showed the best effect in the extraction process of DES, forming the maximum interaction energy of 1575.8 kJ/mol. Additionally, multivariate analysis is employed to establish the relationship between different variables and interaction energy. This study provides micro-theoretical support for the extraction of flavonoids and polyphenols.