A single-phase PuNi3-type Nd2MgNi9 alloy was firstly prepared through induction melting followed by zoning annealing method, and the structural and electrochemical properties of the alloy were studied. Low-angle X-ray diffraction and Rietveld refinement analyses verify that the crystal structure of the Nd2MgNi9 alloy is the PuNi3-type super-stacking structure with a space group R-3m. It is found that the Nd2MgNi9 alloy electrode exhibits excellent electrochemical properties. The discharge capacity of the alloy electrode is 370.6 mAh g−1 and its high rate dischargeability reaches up to 49.6% at a 1440 mA g−1 discharge current density. Especially, the cyclic stability is heightened to 92.1% at the 100th charge/discharge cycle and retains 79% at the 300th charge/discharge cycle, which are significantly better than those of the PuNi3-type La2MgNi9 alloy. On the basis of the R-3m crystal structure calculation results, we found that the single-phase Nd2MgNi9 alloy has the smaller volume deformation rate ΔV/V (+1.19%) and lower lattice strain (0.3180(3)%) after hydrogenation/dehydrogenation, resulting in the weaker pulverization degree of the alloy particle and minor oxidization/corrosion of active material.