Helicon plasma sputtering has been used to prepare Fe/Si MLs with an Fe layer thickness around tFe=2–5 nm for a Si spacer fixed at the thickness of tSi=1 and 1.5 nm. Present study found that the Fe/Si MLs of the Si spacer thickness at tSi=1 nm exhibit antiferromagnetic nature, but the other Fe/Si MLs are ferromagnetic. The maximum value of magnetoresistance (MR) ratio in Fe/Si MLs appears at tFe=3 nm, tSi=1 nm and is about 0.22%. We performed 400 keV Ar ion irradiation to investigate the behavior of magnetic properties in Fe/Si MLs. The magnetization measurements of Fe/Si MLs after 400 keV Ar ion irradiation show the degradation of antiferromagnetic behavior and the values of MR ratio after ion irradiation decrease. X-ray diffraction (XRD) patterns indicate that the peak intensity of a satellite peak originated in superlattice structure does not change within the range of ion dose used. These results imply that the interface structures after ion irradiation become rough although the superlattice structures remain. Therefore, we consider that the change of MR properties in Fe/Si MLs by 400 keV Ar ion irradiation is due to the thickness dependence of Si layers like metallic superlattice structures.