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Noble-metal electrocatalysts supported by biological-organism-derived carbons have attracted attention from the public due to the growing demands for green synthesis and environmental protection. Carbonization at high temperatures and hydrogen reduction are critical steps in this technical route. Herein, <i>Shewanella oneidensis</i> MR-1 were used as precursors, and the effects of the hydrogen-reduction procedure on catalysts were explored. The results showed that the performances of FHTG (carbonization followed by hydrogen reduction) displayed the best performance. Its ECSA (electrochemical surface area), MA (mass activity), and SA (specific activity) reached 35.01 m² g⁻¹, 58.39 A·g⁻¹, and 1.66 A cm⁻², respectively, which were 1.17, 1.75, and 1.50 times that of PHTG (prepared through hydrogen reduction followed by carbonization) and 1.56, 2.26, and 1.44 times that of DHTG (double hydrogen reduction). The high performance could be attributed to its fine particle size and rich N content, and the specific regulation mechanism was also proposed in this paper. This study opens a practical guide for effectively avoiding particle agglomeration during the fabrication process for catalysts.