Abstract: Because of its unique long range disordered structure and numerous free volume, amorphous alloy is considered to be able to accommodate the damage caused by ion bombardment and has good irradiation resistance. 2 MeV He⁺ ions were selected to irradiate amorphous alloy Fe₈₀Si₇B₁₃, and it was found that the arrangement of atoms in the amorphous alloy became uneven. In the bubble layer located near the He ion range which was about 3.5 μm from the surface, the local atoms had a tendency of ordered arrangement. Under the irradiation, no obvious damage could be observed on the surface of the amorphous alloy, while the surface roughness increased, which reduced the surface relative reflectivity of the amorphous alloy. After the irradiation, the Fe-based amorphous alloy maintained the soft magnetic performance. The variation of atomic arrangement in the amorphous alloy enhanced its saturation magnetic induction intensity.