A size-selected Ar gas cluster ion beam (GCIB) was applied to the SIMS of a polystyrene thin film. The size of Ar cluster ions are selected between 5000 to 500 atoms at an acceleration voltage of 5 and 10 kV using time-of-flight technique. Under this condition, the kinetic energy per constituent atom (Eatom) of the GCIB projectile was estimated to be 1 ∼ 20 eV. The Eatom dependence of secondary ion yield of fragment species of polystyrene can be essentially classified into three types which are attributable to the relationship between the Eatom and the dissociation energy of the specified bonding site of the molecule. These results indicate that the site-specific bond breaking of molecules could be possible by adjusting the Eatom of size-selected GCIB. Copyright © 2010 John Wiley & Sons, Ltd.