The damage properties of Focused Ion Beam(FIB) milling Si3N4thin film are investigated by the detailed analyzing images of nanoholes and simulation of Monte Carlo. The damage depth in the Si3N4thin film for two different ion species(Gallium and Arsenic) under various parameters(ion energy, angle of incidence) are investigated by Monte Carlo method. The simulations show the damage depth increases with the increasing ion energy, the damage depth is dependent on the angle of incident ion, the curves of the damage depth for Ga ion and As ion at 30 keV nearly superpose, while the damage depth for Ga with 90 keV ion is more than that for As ion with the same energy.