Oxygen coordination and vacancy ordering play an important role in dictating the functionality of complex oxides. In this work, an unconventional layering of oxygen ions in a mixed conductor SrCo1‐xFexO3‐δ (SCFO) thin film grown epitaxially on SrTiO3 (STO) is reported. Scanning transmission electron microscopy (STEM) reveals alternating layers of oxygen deficiency along the growth direction, with the oxygen‐rich layer correlated with the neighboring Co,Fe‐site intensity, and contraction of the Sr–Sr distance. Density functional theory (DFT) calculations and STEM image simulations support the emergence of periodic (Co,Fe)O6 and (Co,Fe)O4/(Co,Fe)O5 layers, an ordering that is also sensitive to the Co:Fe ratio.