In this paper, we calculated the defect formation energy of oxygen vacancies with different charge states (0, +1, +2) in beryllium oxide crystal by using density functional theory (DFT). Based on defect formation energy, the positions of charge transition levels are obtained. However, there is a well-known problem that DFT will underestimate the band gap, which leads to the positions of charge transition levels are arguable. To obtain more accurate charge transition levels, we employ the hybrid functionals (HSE) to relieve the band edge problem, as well as use the finite-size corrections (FNV) to correct the defect formation energy. After obtaining the location of the charge transition level, we obtain a reliable description of the optical line shape of the F/F[Formula: see text] center containing electron–phonon coupling. The absorption spectra of the F center and F[Formula: see text] center peak at 7.1 eV and 6.3 eV, respectively. The luminescence band of the F center peaks at 4.7 eV. Furthermore, we speculate that the luminescence band near 3.7 eV is assigned to the F[Formula: see text] center.