Depth profiling has been rarely used with secondary ion mass spectrometry (SIMS) of organic materials, because the primary keV atomic ions produce weak signals for large molecules and often damage them during the etching process. In previous studies, we have found extremely low-damage secondary ion emission from organic materials bombarded with large Ar cluster ions, and proposed to use large gas cluster ions as primary ions for SIMS. In this study, secondary ions were measured with a linear type time-of-flight (TOF) technique, and the application of large Ar cluster ion beams to molecular depth profiling of organic films is demonstrated. The intensities of molecular ions were kept constant, though the primary ion beam fluence exceeded the static SIMS limit. These results indicate that large Ar cluster ion beams could be used as powerful tools for SIMS depth profiling.