To reveal the origin of the CO oxidation activity of Ruthenium nanoparticles (Ru NPs), we structurally characterized Ru NPs through Rietveld refinement analysis of high-energy X-ray diffraction data. For hexagonal close-packed (hcp) Ru NPs, the CO oxidation activity decreased with decreasing domain surface area. However, for face-centered cubic (fcc) Ru NPs, the CO oxidation activity became stronger with decreasing domain surface area. In comparing fcc Ru NPs with hcp Ru NPs, we found that the hcp Ru NPs of approximately 2 nm, which had a smaller domain surface area and smaller atomic displacement, showed a higher catalytic activity than that of fcc Ru NPs of the same size. In contrast, fcc Ru NPs larger than 3.5 nm, which had a larger domain surface area, lattice distortion, and larger atomic displacement, exhibited higher catalytic activity than that of hcp Ru NPs of the same size. In addition, the fcc Ru NPs had larger atomic displacements than hcp Ru NPs for diameters ranging from 2.2 to 5.4 nm. Enhancement of the CO oxidation activity in fcc Ru NPs may be caused by an increase in imperfections due to lattice distortions of close-packed planes and static atomic displacements.