Nanolayered Zr/Nb metals are considered promising for advanced nuclear reactors due to their superior resistance to irradiation. In this study, Zr/Nb multilayers were irradiated with 50 keV He+ ions to a fluence of 1 × 1017 ions/cm2 at temperatures of room temperature, 350 °C, and 500 °C to investigate irradiation-induced structural changes. X-ray diffraction (XRD) analysis indicated low-angle shifts of 0.08-0.54° and high-angle shifts of 0.08-0.42° in the irradiated Zr and Nb layers, suggesting tensile and compressive strains, respectively. At 500 °C, the selected-area electron diffraction (SAED) observed a 9.2% lattice expansion in Zr and a 0.13% contraction in Nb. Geometric phase analysis (GPA) revealed varying strain distributions, transitioning from incoherent to coherent interfaces with increasing irradiation damage. Transmission electron microscopy (TEM) identified the presence of He bubbles in the Zr layer as one of the reasons for strain differences. Nanoindentation tests showed an increase at a depth of 150 nm hardness of 0.831 GPa at 500 °C compared to 350 °C. These results are attributed to differences in crystal structure, vacancy dynamics, interfacial effects, and lattice strain influences. Stability of Zr/Nb interfaces after He irradiation was studied. This study provides insights into the radiation behavior of Zr/Nb nanoscale metallic materials, enhancing our understanding of their potential as structural materials in nuclear energy systems.