Nanoscale amorphous yttrium–iron–garnet (YIG) particles were prepared by the alkoxide method. They were dispersed in a kerosene solvent, coated on a quartz plate substrate, and calcined at a temperature of 1273 K for 2 h. Surface morphology and cross-sectional microstructure of the thin coated films were examined by atomic force microscopy and transmission electron microscopy, respectively. During the calcination, amorphous YIG particles were transformed to YIG nanocrystals of ≈25 nm in mean diameter, and no extended grain growth or fusion of the multigrains was observed. Each particle was individually crystallized, but interconnected to each other, forming a sponge-like structure of 600 nm in thickness. Electron diffraction and energy dispersion x-ray analysis verified that the sponge-like layer consisted of YIG nanocrystalline particles. A rather dense intermediate layer of ≈100 nm in thickness was formed as a result of interfacial reactions between YIG and SiO2 decomposing to α-Fe2O3 and Y2Si2O7. The change in the Si concentration across the interlayer depth was modeled by thermal diffusion. This peculiar sponge-like structure of YIG nanoparticles supports our previous interpretation of the shift of the light absorption spectral peak, i.e., due to this peculiar structure, electrons are localized in each YIG particle, which act as a quantum dot, attributing to the quantum size effect observed in the spectral shift.