A systematic theoretical investigation included 39 kinds natural alkannin derivatives were performed by means of quantum chemical computation method. The ionization potential(IP), electronic affinity (EA) and bond disassociation energy(BDE) of the hydrogen atom in the hydroxyl(O-H) were calculated. The relationship between these physical quantities and the hydroxyl-free radical scavenging activities were analyzed, including the spin density of 5-, 7-, 9-site carbon in the compounds and O14, O16 oxygen, and the effect of EA of molecules on the antitumor activity. The research proves that introducing side chain and unsaturated bond will lead to the decrease of BDE, IP and EA values. All these changes will result in the increase of free radical scavenging activities, which shows that the effect of antineoplastic activity will become more obvious. While introducing large volume group into branch of side chain groups will increase of BDE and IP of the compounds.