Ion-induced damage on organic materials has been evaluated with secondary ion mass spectrometry (SIMS). However, conventional sputter beams, such as SF5+, C60+ cannot etch the organic materials without inducing damage, and it is difficult to evaluate the depth distribution of the damage in these materials. Large gas cluster ion can etch organic materials without damage, and in this study the damaged layer thickness was evaluated by molecular depth profiling with Ar cluster ion beam. Arginine films were irradiated with 10 keV Ga+ at a dose of 1.0 × 1014 ions/cm2 with the aim of forming a damaged layer on the surface. The chemical structure of arginine was seriously damaged, as indicated by the non-detection of protonated arginine molecular ions after Ga+ ions irradiation. The peak intensity of the protonated arginine ion increased with increasing sputtering depth and saturated at the depth of about 30 nm. This value agreed with the projection range of the Ga+ ion indicating that the depth of the ion-induced damage was the same as projection range of the ion. Ion-induced damage layer thickness on arginine films were accurately evaluated by molecular depth profiling with Ar cluster ion beam.