The availability of aberration correctors for the probe-forming lenses makes simultaneous modification and characterization of materials down to atomic scale inside a transmission electron microscopy (TEM) realizable. In this work, we report on the electron-beam-induced reconstructions of three types of antiphase boundaries (APBs) in a probe-aberration-corrected TEM. With the utilization of high-angle annular dark-field scanning transmission electron microscopy (STEM), annular bright-field STEM, and electron energy-loss spectroscopy, the motion of both heavy element Mn and light element O atomic columns under moderate electron beam irradiation are revealed at atomic resolution. Besides, Mn segregated in the APBs was observed to have reduced valence states which can be directly correlated with oxygen loss. Charge states of the APBs are finally discussed on the basis of these experimental results. This study provides support for the design of radiation-engineering solid-oxide fuel cell materials.