Raman spectra analysis has been carried out for both the as-sintered and annealed Ba[(Mg1−xNix)1/3Nb2/3]O3 ceramics. Based on the harmonic resonant model, all the Raman modes are successfully assigned according to the effects of ion substitution and post-densification annealing. All of the as-sintered samples present 7 normal modes as predicted by factor group analysis; an extra mode at around 560 cm−1 exists in x = 0.6-1.0. The 3 modes Eg(O), Eg(Nb), A1g(Nb) between 150-350 cm−1 decrease in intensity with increasing x, agreeing well with the variation of ordering degree. By post-densification annealing for x = 0.4, a strong dependence on ordering degree has been proved for the A1g(O) mode at around 790 cm−1. For the as-sintered samples, the Q × f value correlates well with the oxygen octahedron stretch mode A1g(O), while the dielectric constant εr is dominated by ionic polarizability rather than the rigidity of the oxygen octahedra. After annealing, the Raman modes are intensified, corresponding to the enhancement of cations ordering. The annealing significantly increases the A1g(O) Raman shift and decreases the FWHM (full width at half maximum) of A1g(O) mode, resulting in the increase of εr and the improvement of Q × f value for each composition. The intensity ratio of A1g(Ba)+Eg(Ba) mode to A1g(O) mode increases after annealing, implying that A1g(Ba)+Eg(Ba) is more dominant in the ordered structure.