The order-disorder states of the A-site vacancy of PBN solid solution affected by different thermal treatments were studied with the aid of High Resolution Electron Microscopy (HREM). PBN ceramics around the morphotropic phase boundary were prepared through two routes to control ordering degree of the A-site vacancy: (1) samples through quenching processes resulted in chaotic states of the A-site vacancies and misfit anti-phase boundary; (2) samples through slow cooling led to an ordered structure of the vacancies in the A1-site. The ordered A1-site vacancies were modulated by interchanges of the sublattices of the ordered vacancies and the Pb2+ cations in the A1-sites along both and orientations, forming a narrow discommensurate wall between two anti-phase domains. The anti-phase domains were observed as a regular belt structure with dimensions of about 45 nm × (≥120) nm. The belt nano-domain structures were a result of quasi-equilibrium thermodynamic processes.