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-based oxides.