The internal structure of PbSe nanocrystals was deduced using synchrotron X-ray photoemission spectroscopy for three different sizes of nanocrystals. The photoemission data revealed the layered structure of PbSe nanocrystals with the crystalline PbSe core surrounded by a nonstoichiometric Pb1-xSe shell, finally passivated by a capping agent in the outermost layer. A detailed analysis of the experimental data yielded quantitative information on the thickness of three different layers, which is unavailable through any other technique; moreover, the overall sizes of the nanocrystals probed by transmission electron microscopy were in agreement with the corresponding quantity obtained in the present experiment. The present results provide a plausible explanation for the strong variation in the photoluminescence intensity with size observed for these nanocrystals.