Hydroxyanthraquinones (HAQs) have a significant antioxidant activity. In this study, the thermodynamic parameters, frontier molecular orbitals, and dynamic process of HAQs scavenging free radicals were systematically evaluated by density functional theory, and the results were verified by in vitro experiments. The results indicated that, in gas and benzene systems, the hydrogen atom transfer (HAT) was the main mechanism in the antioxidant process of HAQs because the bond dissociation enthalpies were much lower than the ionization potentials (IPs) and proton affinities. The polarity of the solvent (ethanol and water) led to a significant decrease of IPs, and the single electron transfer followed by proton transfer mechanism was the main mechanism. Furthermore, polar solvents were more conducive to the antioxidant activity of HAQs than non-polar solvents. Moreover, the antioxidant activity of HAQs increased with the increase of the number of hydroxyl groups. However, in the non-polar system, alpha-OH of HAQs was more likely to form hydrogen bonds with neighboring carbonyl O atoms, reducing its contribution to the antioxidation. In the polar system, alpha-OH can enhance the electron-donating ability to increase the antioxidant capacity.