Zr/Nb nanoscale multilayers are regarded as one of the important candidate materials used in next-generation reactors. Understanding structural evolution induced by ion bombardment is crucial for the evaluation of lifetime performance. Magnetron sputter-deposited Zr/Nb multilayers with a periodicity of 7 nm were subjected to 300 keV He ion irradiation with three different fluences at room temperature. The depth-resolved strain and damage profiles in the Zr/Nb multilayers were investigated by grazing incidence X-ray diffraction. The tensile strain was found in the deposited Zr/Nb films. After He ion irradiation, the intensity of diffraction peaks increased. The change in diffraction peaks depends on He fluence and incident angle. Irradiation-induced pre-existing defect annealing was observed and the ability to recover the microstructure was more significant in the Zr films compared to the Nb films. Furthermore, the efficiency of defect annealing depends on the concentration of pre-existing defects and He fluence. When the He fluence exceeds the one for pre-existing defect annealing, residual defects will be formed, such as 1/3<12¯10> and 1/3<11¯00> dislocation loops in the Zr films and 1/2<111> dislocation loops in the Nb films. Finally, introducing deposited defects and interfaces can improve the radiation resistance of Zr/Nb nanoscale multilayers. These findings can be extended to other multilayers in order to develop candidate materials for fusion and fission systems with high radiation resistance.