In recent years graphene and its derivatives, have attracted scientific interest due to their unique properties. This study is to explore the quality of synthesized graphene oxide and reduced graphene oxide foils under the irradiation of protons and helium ions of the same energy and current. Fully characterizations by Raman spectroscopy, Rutherford backscattering spectrometry and Elastic recoil detection analysis and the relative results are presented. The effects of parameters, such as type of ions, their current and irradiation time, are studied. The quality of large-scale fabrication of graphene oxide and reduced graphene oxide (rGO) is important for industrial and research applications of these materials. An overview on the changes in the optical property and electron conductivity of graphene oxide and reduced graphene oxide under irradiation by protons, helium and carbon ions are also summarized.