The magnesium-based metallic alloys have been exhibited to be the improved hydrogen storage materials. In the present investigation, a Nanostructured Mg67Ni33 and Niobium substituted intermetallic compound was prepared by a high-energy ball milling technique for hydrogen storage application. Niobium substitution on the pure crystalline intermetallic compound changed the structure of the crystalline to semi-amorphous as well as changed the interplanar spacing after 30 hours of milling. Furthermore, the effect of Nb substitution on the inter-planar shift and its corresponding implications on lattice strain, crystallite size, and unit cell volume of the Mg2Ni compound were also discussed. Transmission electron microscope studies confirm the particle size was reduced to less than 100 nm for 30 hours of milling. However, SEM images confirm the agglomeration of these nanoparticles and form spherical particles of size around 3-5 µm. XRD and EDS authenticate the presence of oxides. Kissinger’s analysis confirmed that Mg2Ni powder exhibited lower activation energy of 64.101 kJ/mol than niobium-substituted alloy powders. The hydrogen charge and discharge potential of these compounds are discussed in detail.