In this study, we present molecular depth profiling of multilayer structures composed of organic semiconductor materials such as tris(8-hydroxyquinoline)aluminum (Alq3) and 4,4'-bis[N-(1-naphthyl)-N-phenylamino]biphenyl (NPD). Molecular ions produced from Alq3 and NPD were measured by linear-type time-of-flight (TOF) mass spectrometry under 5.5 keV Ar70) ion bombardment. The organic multilayer films were analyzed and etched with large Ar cluster ion beams, and the interfaces between the organic layers were clearly distinguished. The effect of temperature on the diffusion of these materials was also investigated by the depth profiling analysis with Ar cluster ion beams. The thermal diffusion behavior was found to depend on the specific materials, and the diffusion of Alq3 molecules was observed to start at a lower temperature than that of NPD molecules. These results prove the great potential of large gas cluster ion beams for molecular depth profiling of organic multilayer samples.