The dielectric loss tangent at microwave frequencies for the complex perovskite Ba(Zn1/3Ta2/3)O3was calculated with respect to the degree of structural disorder on B sites. Starting out from the equations of ion motion, dielectric loss was expressed in terms of the pair‐correlation functions corresponding to the ordering of Zn and Ta ions on B sites. The characteristic length included in the pair‐correlation functions corresponds to the average size of the region containing disorder in ion arrangements on B sites; thus the relation between the structural disorder on the B site and the dielectric loss tangent at microwave frequencies was clarified theoretically. The numerical results show that the microwave loss tangent values change their power from – 3 to – 6 with increasing degree of order on the B site, which agrees well with the experimental observations. Results obtained here confirm the physical origin of the microwave loss of complex perovskite Ba(Zn1/3T