Abstarct: In this research, the plasma etching process of graphene sheet laxyered on SiO2 substrate is investigated. The graphene sheet is bombarded with oxygen ions and the simulation is performed by molecular dynamics using LAMMPS software. In this simulation, in order to investigate the effect of the energy of the incoming ions on the graphene sheet etching process, the ion energies are changed from 3 to 12 eV, respectively. Also, the flux changes between the two values. The results show that by increasing the energy of the bombarding ions from 3 to 12 eV, the number and size of holes created in the graphene sheet increase. By defining the damage parameter, Db, as the fraction of broken C-C bonds in the graphene sheet, we determined the degree of damage to the graphene surface. The value of this parameter in different energies and fluxs for graphene sheet was between 0 and 1. The results show that with increasing the energy of the bombarding ions from 3 to 12 eV and also increasing the flux of ions from f0 (9 oxygen) to 2f0 (18 oxygen), the number and size of holes created in the graphene sheet have increased. The maximum value of damage parameter in flux f0 was between 0 and 0.04 and for flux 2f0 was between 0 and 0.06. Value of damage parameter has increased withtime, energy and flux of incoming particles. Examination of the radial distribution function (RDF) before and after bombardment shows that the etching has caused irregularities in the structure of graphene. Also, the average number of C-C bonds in graphene decreases with increasing energy of the input oxygen atoms, which indicates the loss of carbon bonds with increasing energy. Also, the results show that at 3 eV energy the damage to the graphene sheet is negligible. It should be noted that in this simulation, which uses the Reax force field, we have witnessed the formation of O2, CO, CO2, C2O2 and CO3 species.