Ceramics of 0.35Ba(Ni1/3Nb2/3)O3–0.65Ba(Zn1/3Nb2/3)O3 were prepared by the mixed oxide route. The effect of the cooling rate (2 °C–240 °C/h) after sintering on the microwave dielectric properties of the ceramics was examined. While the extrinsic factors, such as porosity and secondary phases, markedly influence the dielectric properties in the low-frequency regime, they have minimal effect on these properties in the high-frequency regime. The mechanisms involved in modifying the high-frequency dielectric properties of the materials were investigated by Fourier transform infrared and Raman spectroscopy, in conjunction with the Rietveld analysis of x-ray diffraction (XRD) spectra. A reduction in the cooling rate after sintering results in an increase in the high-frequency Q×f (product of dielectric Q value and measurement frequency) from 42 to 58 THz in the high-frequency regime (∼1.5 THz). Such behavior correlates very well with the increase in the B-site occupancy by Nb (deduced from the Rietveld analyses of XRD spectra) and the increase in the coherency of the lattice vibration (deduced from the reduction in the full-width-at-half-maximum of the A1g(O) Raman mode). In contrast, the cooling rate after sintering has very limited effect on the relative permittivity (varying from 40.8 to 41.9 at 1.5 THz), which is in accord with the phenomenon that the cell volume and the Raman shift of A1g(O) Raman mode are essentially independent of the cooling rate.