The electronic structures of QHS and DQHS were completely optimized and calculated by B3LYP density functional theory at the 6-31g* level.The relationship between electronic structure parameters and antimalarial activity was discussed.There exists significant difference in frontier orbitals of QHS and DQHS.Their net charges and bond orders were also compared respectively.The results of calculation prove theoretically that the endoperoxy bridge is the essential of antimalarial activity.The difference of antimalarial activity between QHS and DQHS was reasonably explained based on their electronic structures.