Large gas cluster ion beam technology answers expectations in the field of material modification, because it provides unique capabilities, such as atomic-scale surface smoothing, shallow implantation and high sputtering yield. The relationship between incident cluster size and irradiation effects observed with large gas cluster ion beam is not yet clearly understood, and in this work we used size-selected Ar cluster ion beam to study the effects of incident energy-per-atom and cluster size on sputtering and secondary ion emission. Incident Ar cluster ions were size-selected by using the time-of-flight (TOF) method. It was found that the secondary ion yields decreased more rapidly with decreasing incident energy-per-atom and that the threshold energy-per-atom for sputtering of Si and Si⁺ were different, because the ionization energy of Si was higher than the surface binding energy of Si. It indicates that cluster ion irradiation sputtered only neutral Si from the surface by under the specific conditions.