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Two types of cattail flower-derived nanoporous carbon (NPC), i.e., NPC activated with KOH and H₃PO₄, were produced and characterized using several techniques (e.g., Raman spectroscopy, nitrogen adsorption, and X-ray photoelectron spectroscopy). The influence of the carbon support characteristics on the particle sizes and chemical states of Pd in the synthesized Pd/NPC catalysts, which affect the catalytic activity and product selectivity, was analyzed. The surface chemistry properties of NPC were the main factors influencing the Pd particle size; by contrast, the textural properties did not significantly affect the size of the Pd particles on NPC supports. The use of Pd nanoparticles supported on the rich-functionalized surface carbons obtained by H₃PO₄ activation led to superior catalytic activity for the polyunsaturated fatty acid methyl ester (poly-FAME) hydrogenation, which could achieve 90% poly-FAME conversion and 84% selectivity towards monounsaturated FAME after a 45-min reaction time. This is due to the small Pd nanoparticle size and the high acidity of the catalysts, which are beneficial for the partial hydrogenation of poly-FAME in biodiesel. Conversely, the Pd nanoparticles supported on the high-surface-area carbon by KOH activation, with large Pd particle size and low acidity, required a longer reaction time to reach similar conversion and product selectivity levels.