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As a Pt-group element, Pd has been regarded as one of the alternatives to Pt-based catalysts for the hydrogen evolution reaction (HER). Herein, we performed density functional theory (DFT) computations to explore the most stable structures of Pd<i>_x</i>B<i>_y</i> (<i>x</i> = 6, 19, 44), revealed the in situ structural reconstruction of these clusters under acidic conditions, and evaluated their HER activity. We found that the presence of B can prevent underpotential hydrogen adsorption and activate the H atoms on the cluster surface for the HER. The theoretical calculations show that the reaction barrier for the HER on ~1 nm sized Pd₄₄B₄ can be as low as 0.36 eV, which is even lower than for the same-sized Pt and Pd₂B nanoparticles. The ultra-high HER activity of sub-nanosized Pd<i>_x</i>B<i>_y</i> clusters makes them a potential new and efficient HER electro-catalyst. This study provides new ideas for evaluating and designing novel nanocatalysts based on the structural reconstruction of small-sized nanoparticles in the future.