W(Mo, 9.8 at.%)/Cu nanometer multilayer films of different individual layer thickness were prepared by RF magnetron sputtering, which were irradiated by 60 keV He+ ions at ion fluence from 0 to 51017 He+/cm2. Microstructures of nanometer multilayer W(Mo)/Cu films were investigated by high-resolution transmission electron microscope (HRTEM) and X-ray diffraction (XRD) before and after irradiation. Experimental results indicate that: (1) The phase transformation of -W (A-15) into steady state -W can be attributed to the bombardment effect of energetic He ions on the surface of films, leading to phase-transition temperature during irradiation. (2) The irradiation tolerance of W(Mo)/Cu multilayer film was found to depend on the individual layer thickness. (3) At the fluence of 51017 He+/cm2, the HRTEM results reveal that the behavior of helium cluster/bubble in the W(Mo) film is obviously different from that in the Cu film. It is interesting that the distribution of helium cluster/bubble is related to the grain orientation of W(Mo) film and tends to distribute along W (211) plane. However, Cu film is completely amorphized and helium cluster/bubble is evenly distributed in it.