Studies on effects of di-F-substitution sites in the main ligand (dpq) of complex [Ru(bpy)2(dpq)]2+ (dpq=dipyrido [3,2-d:2′,3′-f] quinoxaline, bpy=2,2′-bipyridyl)) are carried out by using the DFT method at the B3LYP/LanL2DZ level. The effects caused by the electron-withdrawing group (F) on different sites of the electronic structures and the related properties, e.g. the components and energies and of some frontier molecular orbitals, the spectral properties, the net charge populations of some main atoms of the complexes, and the relative stabilities of isomers, etc., have been investigated. The results show that di-F-substitution sites have some interesting effects. First, the di-F-substitution on any site of main ligand(dpq) can make the components of the LUMO of the derivative mainly distribute in the main ligand, whereas those of the LUMO in the parent complex I mainly distribute on the co-ligands, and then we can say that the di-F-substitution can activate the main ligand and passivate the co-ligands of the derivatives in the first excited states. Second, 7,7′-di-F-substitution makes the energy of LUMO greatly reduce and that of HOMO almost stay unchanged, and then the affinity of the isomer binding to DNA must be the greatest, and the wave-length of the ground band of this isomer must be the greatest too. In addition, the atomic charge populations on main ligand, the relative stabilities of isomers and coordination bond lengths are also discussed. The above theoretical results are useful references to the functional molecular designs of the complexes and the analysis of the interaction mechanism of the complexes with DNA, etc.