The nucleation of noble metal nanoparticles on oxide surfaces can lead to dramatic enhancements in catalytic activity that are related to the atomic-scale formation of the nanoparticles and interfaces. For the case of submonolayer Pt deposited on the 2×1 SrTiO(3)(001) surface atomic-force microscopy shows the formation of nanoparticles. We use X-ray standing wave (XSW) atomic imaging to show that these nanoparticles are composed of Pt face-centered-cubic nanocrystals with cube-on-cube epitaxy laterally correlated to the substrate unit cell. The phase sensitivity of the XSW allows for a direct measurement of the interface offset between the two unit cells along the c-axis. Different Pt coverages lead to differences in the observed XSW image of the interfacial structure, which is explained by a proposed model based on the Pt-Pt interaction becoming stronger than the Pt-substrate interaction as the global coverage is increased from 0.2 to 0.6 ML.