Controlling particle size and structure is challenging in the synthesis of composite metal oxide nanoparticles. In this study, first-principles calculations based on density functional theory were used for perovskite-type composite oxides to elucidate the structure of nanoclusters, and it was revealed that their surface energy strongly depends on the constituent cations of the composite oxides. Particle size variation observed in supercritical hydrothermal synthesis can be explained by factors included in the simulation, such as surface composition variance, surface reconstruction, and the resulting difference in surface energies of the composite oxides. Structural differences between the bulk and nano forms were investigated using X-ray diffraction and X-ray absorption spectra. Lattice expansion and structural distortion were observed in the synthesized nanoparticles compared to the bulk crystal. These experimentally measured characteristics in the local structure were qualitatively reproduced by the cluster calculations, facilitating the understanding and prediction of nanoparticle formation.