AbstractA precise investigation of NbO has been carried out by advanced electron microscopy combined with powder and single crystal X‐ray diffraction (XRD). The structure of pristine NbO has been determined as Pm‐3 m space group (SG) with a = 4.211 Å and the positions of Nb and O at the 3c and 3d Wyckoff positions, respectively, which is consistent with previous report based on powder XRD data. Electron beams induced a structural transition, which was investigated and explained by combining electron diffraction and atomic‐resolution imaging. The results revealed that the electron beam stimulated both Nb and O atom‐migrations within each fcc sublattice, and that the final structure was SG Fm‐3 m with a = 4.29 Å, Nb and O at the 4a and 4b with 75 % occupancy and same chemical composition. Antiphase planar defects were discovered in the pristine NbO and related to the structural transformation. Theoretical calculations performed by density functional theory (DFT) supported the experimental conclusions.