This study investigates the effect of CaZrO3 (CZ) substitution on the evolution of an ordered structure in a Ca(Mg1/3Nb2/3)O-3 (CMN) system using Raman spectroscopy, X-ray diffractometry, and transmission electron microscopy. It indicates that a (1-x) CMN-(x)CZ solid solution has the 1:2 and 1:1 ordered structure distorted by the antiphase, the inphase tilting of oxygen octahedra, and the antiparallel shift of A-site cation. A distinct correlation is noted between the transition of the ordered structure and microwave dielectric properties. The differences in epsilon(r) and tau(f) are attributed exclusively to the differences in the type of cation arrangement. The structure with the 1:2 ordering exhibits a lower relative permittivity and a more negative tau(f) than the structure with the 1:1 ordering. The increased fraction of compressed Nb-O bond in the 1:2 ordered structure associated with a large NbO6 octahedral distortion is correlated with a decrease in relative permittivity and change of tau(f) toward more negative values. Simultaneously, the substitution of the Zr4+ ion causes a linear increase in polarizability, and it also results in an increase in the relative permittivity.