Recently, water and some other molecules are applied to the massive cluster projectiles for SIMS to improve the secondary ion yields by chemical effects. The ionization probability should be influenced by the properties of the primary ion beams as well as the chemical nature of the sample surface. However, the mechanisms of ionization by the large cluster collision is still unclear. In this study, we have generated water, methanol and methane molecular cluster ion beams and investigated the secondary ion emission from amino acid thin films bombarded by the molecular cluster ion projectiles.