The development of efficient catalytic hydrodeoxygenation (HDO) processes for vanillin offers a promising but technically demanding approach to generating 2-methoxy-4-methylphenol (MMP). The as-prepared Pd₁Fe₂₀/graphitic carbon nitride (g-C₃N₄) single atom catalyst was synthesized by photo-deposition strategy and enabled the HDO to obtain conversion 99% and MMP selectivity of 99%, achieving a turnover frequency (TOF) of 2033 h⁻¹. Characterization via X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) confirmed the existence of Fe clusters, Pd single atoms, and a well-defined Pd–Fe₃ coordination. Density functional theory (DFT) simulations further provided insights into the electronic configuration of the Pd sites, demonstrating that the Pd–Fe₃ interaction strengthens substrate adsorption and reduces the energy barrier for the rate-limiting step. This study not only addresses the overreliance on precious metals but also establishes a guided approach for designing single atom catalysts for the conversion of biomass-derived feedstocks.