The degree of Zn 2+ and Ta 5+ ions ordering could play an important role in the dielectric loss in Ba(Zn 1/3Ta 2/3)O 3 (BZT) ceramics. However, the influence of the grain size of Ba(B′ 1/3B″ 2/3)O 3 ceramics with nano or sub-micron grains on the ordering domains structure is still not clear. In the present paper, highly dense (~98%) BZT microwave dielectric ceramics with homogeneous sub-micron structure (~330 nm) were prepared through spark plasma sintering (SPS). High resolution transmission electron microscopy combined with X-ray diffraction (XRD)clearly showed that the B-site ordering structure of sintered BZT samples by SPS becomes the B-site long-range 1:2 ordering as annealing proceeds. In contrast, the short-range 1:2 ordering in non-annealed counterparts was also present, which was not detectable by XRD. The size of B-site ordering domains enlarged with annealing temperature. The sub-micron structure of sintered BZT ceramics by SPS remained stable at up to 1400 C; however, the size of B-site 1:2 ordering domain was more than five times larger, which led to a significant increase of the quality factor ( Q·f) to 37,700 GHz from 15,000 GHz.