Multilayer nanostructure analysis has been carried out for core-shell PbS/EuS nanocrystals by the combination of the synchrotron small-angle X-ray scattering (SAXS) method and energy-dispersive X-ray spectroscopy (EDS). SAXS patterns of a dilute hexane solution of the PbS/EuS nanocrystals were measured at a high signal-to-noise ratio by using synchrotron radiation. Initial structure models used for SAXS data analyses were obtained from EDS images of the particle where Eu and O atoms are localized only in the shell part of a quasi-cubic particle and, on the other hand, Pb and S atoms in the core. By simulating the intensity of SAXS using multilayer-cubic models with various core-shell electron density distributions, it was found that the particle structure was explained approximately as a trilayer-cubic model having the PbS core and the EuS/Eu2O3 shell. The diagonal length of the cubic particle was ca. 9.4 nm and the estimated thicknesses of EuS and Eu2O3 layers in the shell were ca. 1.9 and 2.9 nm at maximum, respectively.