In this paper, the electronic structures and absorption spectra of Co doped and Co, Zn co-doped LiNbO3 crystals are studied by the first-principle using the density functional theory, to explore the characteristics of charge transfer in Co, Zn co-doped LiNbO3 crystals, and to build the relationship between these characteristics and the holographic storage quality. The basic model is built as a supercell structure of 211 of near-stoichiometric pure LiNbO3 crystal with 60 atoms, including 12 Li atoms, 12 Nb atoms and 36 O atoms. Four models are established as the near-stoichiometric pure LiNbO3 crystal (LiNbO3), the cobalt doped LiNbO3 crystal (Co:LiNbO3), the zinc and cobalt co-doped LiNbO3 crystal Co:Zn(L):LiNbO3 with doping ions at Li sites, and the other zinc and cobalt co-doped LiNbO3 crystal Co:Zn (E):LiNbO3) with zinc ions at Li sites and Nb sites. The last two models would represent the concentration of Zn ions below the threshold (6 mol%) and near the threshold, respectively. The charge compensation forms are taken as CoLi+-VLi-, CoLi+-ZnLi+-2VLi- and CoLi+-ZnNb3--2ZnLi+ respectively in doped models. The results show that the conduction band and valence band of pure LiNbO3 crystal are mainly composed of O 2p orbit and Nb 4d orbit respectively, and energy gap is 3.48 eV. The band gap of the doped LiNbO3 crystal is narrower than that of pure LiNbO3 crystal, due to the Co 3d and Zn 3d orbit energy levels superposed with that of O 2p orbit energy levels, and thus forming the upside of covalent bond. The band gap of Co:LiNbO3 crystal is 3.32 eV, and that of Co:Zn:LiNbO3 crystals are 2.87 eV and 2.75 eV respectively for Co:Zn(L):LiNbO3 and Co:Zn(E):LiNbO3 model. The Co 3d orbit is split into eg orbit and t2g orbit with different energies. The absorption peak at 2.40 eV appears in the band gap of Co:LiNbO3 crystal, which is attributed to the transfer of the Co 3d splitting orbital t2g electrons to conduction band. The absorption peaks of 1.58 eV and 1.10 eV could be taken as the result of eg electron transfers of both Co2+ and Co3+ in crystal, especially the latter ion. These two absorption peaks are obviously enhanced in Co:Zn (E):LiNbO3 crystal compared with in other samples in this paper. Based on that, it could be proposed that a charge transfer between Zn2+ and Co2+ as Co2++Zn2+Co3++Zn+ exist in the crystal, which results in the decrease of eg orbital electron number, but hardly affect the t2g orbital electron. The Co ion in crystal could act as the deep-level center (2.40 eV) or the shallow-level center (1.58 eV) with the different accompanying doped photorefractive ions in the two-light holographic storage applications. In both cases, the choice of Zn ion concentration near threshold could be helpful for the photo damage resistance and recording light absorption in storage applications.