The reaction mechanism of 12 antimalarial artemisinin compounds with two competitive pathways was studied by means of quantum chemical calculations using the IMOMO(B3LYP/6-31(d,p):HF/3-21G) method. The oxygen-centered radicals, carbon-centered radicals, and transition states (TS) in both pathways were geometrically optimized. The obtained kinetic and thermodynamic energy profiles show that homolytic C-C cleavage reaction (pathway 2) is energetically more preferable than an intramolecular 1,5-hydrogen shift process (pathway 1), which is consistent with the docking calculations. However, compounds that can easily proceed along the pathway 1 have high activity. Therefore, both pathways are important for antimalarial activity. Moreover, effective discrimination between high and low activity compounds using EA1, deltaE1, and deltaE(1A-2A) was accomplished.