The large-scale and engineering preparation of NiPd powder with an excellent structure is crucial for promoting the development of catalytic applications and the utilization of hydrogen energy. In this study, micro-nano dual-size NiPd alloy with a flake-like microstructure was synthesized using a simple and efficient high-energy ball milling method. Micro-structural analysis was performed on samples at various stages of ball milling to investigate the atomic migration and refinement mechanisms during the process. The microstructure and elemental distribution at different stages of particle refinement were examined, and the particle size distribution of NiPd alloy at varying ball milling times was statistically analyzed. The NiPd alloy produced using this method exhibits two distinct structural features: a flake-like polycrystalline structure and a dual-size nanocrystalline structure. A flake-like polycrystalline powder was achieved using relatively short ball milling durations and characterized by a polygonal two-dimensional structure with a single particle aspect ratio of 24. After 60 h of ball milling, the NiPd alloy developed a dual-size nanocrystalline structure. Under a high ball-to-powder ratio, the average particle size of the alloy decreased to 3.6 μm, more than tenfold smaller than the initial size. The alloy particles transformed from their original elemental metals into alloy phases, with nanoscale alloy particles (approximately 158 nm) adhering to micrometer-sized alloy particles. Additionally, the influence of the ball-to-powder ratio on the refinement process and outcomes was investigated, indicating that a higher ball-to-powder ratio can effectively improve preparation efficiency by accelerating the ball milling process and reducing the final particle size of the NiPd alloy at each milling stage.