Atomic compositions and molar extinction coefficients of PbSe semiconductor nanocrystals were determined by atomic absorption spectrometry, UV-vis-NIR spectrophotometry, and transmission electron microscopy. The Pb/Se atomic ratio was found to be size-dependent with a systematic excess of Pb atoms in the PbSe nanocrystal system. Experimental results indicated that the individual PbSe nanocrystal was nonstoichiometric, consisting of a PbSe core and an extra layer of Pb atoms. For these nonstoichiometric PbSe semiconductor nanocrystals, we proposed a new computational approach to calculate the total number of Pb and Se atoms in different sized particles. This calculation played a key role on the accurate determination of the strongly size-dependent extinction coefficient, which followed a power law with an exponent of approximately 2.5.