The outermost surface of the human hair is covered with a thin layer of fatty acids bonding proteins, which plays an important role in giving hair a soft and smooth feeling and surface hydrophobicity. In this study, changes in fatty acids and protein fragment ions were characterized using time-of-flight secondary ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy (XPS) to investigate hair damage. As a result, the intensity of the fragment ion m/z 76 related to cystine and cysteine, major components of hair keratin, decreased with the hair damage, which is consistent with generation of cysteic acid caused by oxidative cleavage of both thioester bond in the fatty acids and disulfide bond of cystine. Thus, it is indicated that hair damage can be evaluated by measuring m/z 76. Furthermore, 18-methyleicosanoic acid, the major component of the fatty acids, decreased rapidly in three bleaching processes, and the peak at m/z 76 also decreased correspondingly. These results suggest that the oxidative cleavage of thioester bonds in the fatty acids is the major change caused by the bleaching process.