A size-selected gas cluster ion beam (GCIB) system has been developed to study the size effects of energetic large cluster ion bombardments on a solid surface for the first time. This system equipped a permanent magnet with a magnetic flux density of 1.2 T. There is a sliding detector and sample holder on a guiding rail perpendicular to the incoming cluster beam axis. By locating a sample at a certain position, particular size of cluster ion can be irradiated continuously with affordable ion current density. When the total acceleration energy of Ar-GCIB was 5keV, both amorphous and oxide thickness on Si substrate increased with decreasing cluster size. This result showed good agreement with that obtained from molecular dynamics simulations.