Electron spectro-microscope equipped with a parallel-EELS is a powerful tool for elemental analyses as well as an investigation of electronic structures on a local specimen area. The present paper shows an application of this method to organic crystals. Electron energy-loss near-edge structures (ELNES) observed on the carbon and the nitrogen K-edges of the chlorinated Cu-phthalocyanine and poly GeO-phthalocyanine were measured as a function of irradiation dose. From an analysis of the change of ELNES peaks, a sitedependent process in the radiation damage was proposed, which was realized due to the localized property of an inner-shell electron excitation.