Secondary ion mass spectrometry (SIMS) has become a powerful tool for a chemical imaging of surfaces. In particular, cluster ion beams have been widely implemented with SIMS using spatial distributions of molecules as an analysis and imaging method for a sample composed of organic molecules. In this study, we developed a home-built time-of-flight (ToF)-SIMS instrument and generated organic molecular cluster ion beams ionized by multiphoton ionization (MPI) as a primary ion beam. Further, the sample stage loaded with rhodamine 6G was bombarded with size-controlled toluene cluster ions to produce secondary ions. Mass spectra of rhodamine 6G were acquired as a function of the size of toluene cluster ions. We plotted the fragments-to-parent ion ratio against each size of cluster ion, and we found that an intact rhodamine 6G signal would be observed with less fragmentations using (Tol)(n) (> 18)+. We expect this combination of the organic molecular cluster ion beam generated by MPI and ToF-SIMS to greatly expand the field of surface analysis.