Components on the outermost hair surface were directly analyzed with time-of-flight secondary ion mass spectrometry (TOF-SIMS). The depth profiling of characteristic amino acid components in hair surfaces was performed using a Bi3++ analysis beam combined with a C60 ++ sputtering beam. The depth analysis of a protein bilayer model of zein and casein layers indicated that the damage caused by C60++ sputtering did not influence the TOF-SIMS analysis, therefore, the C60 sputtering is considered to be feasible at an analysis depth of 2 µm from the surface. The depth profiling analysis data for hair surfaces showed oscillating changes in the peak intensities of amino acid fragments, and this phenomenon is considered to reflect the multilayer structure of cuticle tissue. Focusing on the first layer of cuticle tissue, the depth profiling change of the cysteine/cystine-related fragment corresponding to the A-layer, exocuticle and endocuticle of cuticle tissue was consistent with the TEM result. Furthermore, a comparison of the depth profiling data from before and after the bleaching treatment revealed that the cysteine/cystine-related peak intensity was high at the outermost surface because the layer was cysteine-rich for bonding the lipid layer. As a result, the existence of a thin protein layer with specific amino acid components, known as the epicuticle, was suggested. The depth profiling analysis of protein using TOF-SIMS provides significant information for investigating the structure and functions of the surface of human hair.