The boundaries of 1:2 ordered domains in Ba[(Co, Zn, Mg)1/3Nb2/3]O3 perovskite ceramics are comprehensively studied by high‐resolution transmission electron microscopy (HRTEM) on the base of atomic position simulation. The atomic configurations for four types of twin boundaries are determined. A‐type and B‐type boundary, which lie along (001)c and (110)c planes, respectively, are conservative. C‐type boundary parallels to (111)c plane, while Г‐type boundary is perpendicular to (111)c plane. At C‐type and Г‐type boundary, atomic intersection leads to a buffer layer, among which the B‐site cations are generally disordered. The width of Г‐type boundary is larger than that of C‐type boundary, so is the perturbation to the system. The energy of four types of twin boundaries is proved to be “A‐type & B‐type < C‐type < Г‐type” according to the magnitude of the destabilization to the system. Single antiphase boundary (APB) is considered to be nonconservative. However, when combined with conservative twin boundary, an extra ordered structure with a periodicity of 1.24 nm along [001]c direction and a periodicity of 0.87 nm along [110]c direction forms. The boundary regions are indeed stabilized by the new superlattice.