The physical vapour deposition of Ni atoms on α-Fe(001) surface under different deposition temperatures were simulated by molecular dynamics to study the intermixing and microstructure of the interracial region. The results indicate that Ni atoms hardly penetrate into Fe substrate while Fe atoms easily diffuse into Ni deposition layers. The thickness of the intermixing region is temperature-dependent, with high temperatures yielding larger thicknesses. The deposited layers are mainly composed of amorphous phase due to the abnormal deposition behaviour of Ni and Fe. In the deposited Ni-rich phase, the relatively stable metallic compound B2 structured FeNi is found under high deposition temperature conditions.