Although ion beam technology has frequently been used for introducing defects in graphene, the associated key mechanism of the defect formation under ion irradiation is still largely unclear. We report a systematic study of the ion irradiation experiments on SiO2-supported graphene, and quantitatively compare the experimental results with molecular dynamic simulations. We find that the substrate is, in fact, of great importance in the defect formation process, as the defects in graphene are mostly generated through an indirect process by the sputtered atoms from the substrate.