The crystal structure of BaFe0.9In0.1O3−δ, which was prepared via heating in N2 (BFI010-N2), was evaluated using high-temperature X-ray diffraction (XRD) and in situ convergent-beam electron diffraction (CBED) at room temperature and 700°C. Although the crystal structure of BFI010-N2 at room temperature was assigned to a cubic perovskite-type structure based on the XRD results, the CBED patterns indicated that the space group of its crystal structure was not Pm3m (No. 221), which corresponds to an ideal cubic perovskite. When the temperature was increased to 700°C, the symmetries for the space group of cubic perovskite were directly observed by means of in situ CBED, indicating that the partial ordering and/or clustering of oxide ion vacancies in the BFI010-N2 vanished and that the oxide ion vacancy arrangements became completely random. The change in crystal symmetry agreed with a sudden decrease in the activation energy of oxide ion conduction at 600°C. The crystal symmetry of the BaFe0.9In0.1O3−δ sample that was prepared via heating in O2 (BFI010-O2) and had a decreased δ value was compared with that of the BFI010-N2 sample. It was concluded that the same phase transition also occurred by a decrease in δ, similar to phase transitions caused by increasing the temperature.