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• SCO-LSMO bilayer films are fabricated by PLD technique. • SCO has been defined to be Ima 2 structure. • Domains and stack-fault structures are detected in SCO layer. • A peculiar nanocrystalline embeds in the SCO-LSMO interface. SrCoO 3-δ (0 < δ < 0.5) film has shown great potential in applications for interface engineering of spintronic devices due to its multiformity of crystal structures and magnetic properties. In this work, we have studied the microstructures of SrCoO 3-δ in SrCoO 2.5 -La 0.67 Sr 0.33 MnO 3 (SCO-LSMO) double-layered films by using scanning transmission electron microscopy. Our fabricated SCO film is determined to have a structure with the Ima 2 space group (No. 46). Perpendicular domain and stack-fault structures are observed to coexist in the SCO layer. In the joint of domains, oxygen content remains a constant for octahedra layers but a slight rise for tetrahedra layers. Continuous changes of oxygen content are also detected in the same level layer in the stack-fault region near the domain boundary. Besides, a peculiar nanocrystalline is observed at the interface of SCO-LSMO. The electron energy-loss spectroscopy results show that the Co ions in nanocrystalline have a lower valence, indicating a chemical compositon of SrCoO 2.5-δ (0 < δ < 0.5). [ABSTRACT FROM AUTHOR]