Effects of superlattice ordering and ceramic microstructure on the microwave dielectric properties of complex perovskite-type oxide Ba(Zn1/3Ta2/3)O3 polycrystalline ceramics are studied. The superlattice ordering ratio was controlled by the sintering time at 1350°C. The superlattice ordering of Zn and Ta ions on B sites increased with increasing sintering time until 80h and reached a saturated value of 80%. However, the microwave Q factor of the samples showed a large variation of the same magnitude of the superlattice ordering ratio. This result suggests that the microwave Q factor of Ba(Zn1/3Ta2/3)O3 ceramics depends not only on the superlattice ordering but also on the ceramic microstructure.