In this paper, the physical phenomena of gallium (Ga+) ion impacting monolayer graphene in the nanosculpting process are investigated experimentally, and the mechanisms are explained by using Monte Carlo (MC) and molecular dynamics (MD) simulations. Firstly, the MC method is employed to clarify the phenomena happened to the monolayer graphene target under Ga+ ion irradiation. It is found that substrate has strong influence on the damage mode of graphene. The mean sputtering yield of graphene under 30 keV Ga+ ion irradiation is 1.77 and the least ion dose to completely remove carbon atoms in graphene is 21.6 ion/nm2. Afterwards, the focused ion beam over 21.6 ion/nm2 is used for the irradiation on a monolayer graphene supported by SiO2 experimentally, resulting in the nanostructures, i.e., nanodot and nanowire array on the graphene. The performances of the nanostructures are characterized by atomic force microscopy and Raman spectrum. A plasma plume shielding model is put forward to explain the nanosculpting results of graphene under different irradiation parameters. In addition, two damage mechanisms are found existing in the fabrication process of the nanostructures by using empirical MD simulations. The results can help us open the possibilities for better control of nanocarbon devices.