Applying crystal field theory and irreducible representation method, the completely diagonalized Hamiltonian matrices of 3d8 ion configurations in the trigonal symmetry sites have been established, which include four kinds of microscopic magnetic interactions: spin-orbit interaction, spin-spin interaction, spin-other-orbit interaction and orbit-orbit interaction. Based on the matries, spectral fine structure and zero-field splitting parameters of LiNbO3Ni2+ crystall are calculated. Jahn-Teller effect, and effects of four microscopic magnetic interoctions on crystal spectral and zero-field splitting parameter are investigated. The results show that Jahn-Teller effect exists in this crystal and spin-orbit interaction makes uppermost contribution to energy level and zero-field splitting parameters while calculated values will be closer to the experimental values when the other three interactions are taken into account.