Barium zinc niobate (Ba(Zn1/3Nb2/3)O3) (BZN) complex perovskite has been reported to have special microwave dielectric properties with close relation of its ordered structure. This study investigated the effect of calcination on the evolution of ordered structure and on quality factor with Raman spectroscopy, X-ray diffractometry, and transmission electron microscopy. The results revealed that single calcination at a lower temperature inhibited the growth of the ordered domain during sintering. In contrast, the 1:2-ordered domain in double-calcined BZN powder grew significantly with a higher sintering temperature and a longer soaking time. It is attributed that double calcination caused a higher degree of 1:2 ordering and better homogeneity. At the same time, the quality factor of the sintered ceramic body was highly promoted when using double-calcined powder. A close relation of the quality factor with the size of ordered domain, the degree of 1:2 ordering, and the relative density of BZN ceramics was presented.