The electronic structures and the absorption spectra of the Cu and Mn mono and co-doped LiNbO3 crystals were investigated by first-principles based on the density functional theory. The results show that the impurity energy levels of Cu and Mn doped LiNbO3 crystals appear within the band gaps, which are contributed by Cu 3d orbital and Mn 3d orbital. The band gap of each doped crystal is narrower than that of LiNbO3 crystal. There are three absorption peaks at 2.87 eV, 2.24 eV and 1.73 eV respectively in Cu∶Mn∶LiNbO3 crystal. The first one and last one come from the electron transitions from Cu2+ and Mn2+ level to conduction band respectively. The second one is not photorefractive and relative with the concentrations of Mn3+. Comparing with the Cu∶Fe∶LiNbO3 crystal, the recording center (Cu2+) is deeper in Cu∶Mn∶LiNbO3 crystal. In the two-center holographic recording, it is practicable to take suitable higher concentration of Cu ion in Cu∶Mn∶LiNbO3 crystal to raise the dynamic range and sensitivity via enhancing the refractive-index change. The selecting of accompanying doping ion would affect the storage parameters, even if the recording center ion (deep level) is the same, so it′s necessary to select codoping ions according to the simulating datum of the different samples.