The microstructure evolution and coarsening kinetics of ordered domain depend on the annihilation behavior in ordered metallic materials. In this work, the annihilation phenomenon of nanoscale B2 antiphase domain boundary (APDB), at various compositions and temperatures, is investigated by establishing an atomic phase field approach. The effect of uniaxial compressive stress is also included. Kinetically, the annihilation behavior of nanoscale APDB presents a staged feature during the dynamic evolution process. Qualitatively, the analyses of area and radius reveal that APDB annihilation evolves along a fixed path. Further, the annihilation rate of APDB is characterized by composition and temperature dependence, which is a result of synergy among the temperature, composition and uniaxial compressive stress. Thermodynamically, the energy analyses reveal that solute depletion at the homophase interface acts energetically for the migration of B2-APDB. The uniaxial compressive stress significantly influences the micromorphology, solute depletion and evolution of APDB, which provides theoretical insight for controlling the nanoscale APDB. Moreover, simulation results show reasonable agreement with previous theoretical results.