The nature of magnetic ordering in LaCoO₃ epitaxial thin films has been the subject of considerable debate. We present direct observations of the spin-state modulation of Co ions in LaCoO₃ epitaxial thin films on an atomic scale using aberration-corrected scanning transmission electron microscopy (STEM), electron energy loss spectroscopy (EELS), and ab initio calculations based on density functional theory (DFT) calculations. The results of an atomic-resolution STEM/EELS study indicate that the superstructure is not associated with oxygen vacancies; rather, it is associated with a higher spin state of Co₃⁺ ions and their ordering. DFT calculations successfully reproduced the modulation of lattice spacing with the introduction of spin ordering. This result identifies the origins of intrinsic phenomena in strained LaCoO₃ and provides fundamental clues for understanding ferromagnetism in Co-base oxides.