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Microwave dielectric powder Ba(Ca1/3Nb2/3)O3 with high B-site cation ordering was synthesized by the molten salt method. Neutron powder diffraction (NPD) and Raman scattering spectra were introduced to investigate the variable ordering degree during the sintering process. It was revealed that the as-synthesized Ba(Ca1/3Nb2/3)O3 powder had a nearly completely ordered structure, and the sintered Ba(Ca1/3Nb2/3)O3 presented a bit higher ordering degree based on the detailed quantitative NPD Rietveld full profile fitting. The complete Raman mode assignment for the Ba(Ca1/3Nb2/3)O3 was presented. The phonon bands could also confirm the order–disorder structural model and increasing ordering degree with the increasing sintering temperature. Final microwave dielectric measurements on sintered samples showed the present compound to tailor other dielectric materials for microwave applications with the dielectric properties of εr = 47.11, and Qf = 1389 GHz, and τf was about 113 ppm/°C.