Using natural resources to construct electrocatalysts for biomass conversion and elucidating their catalytic mechanisms are of great significance, but have remained challenging. Here, a series of two-dimensional (2D) biomass-based Pb/PbO@C catalysts with Pb/PbO nanoparticles anchored on carbon nanosheets were synthesized using natural-derived humate as the precursor. By adjusting the carbonization temperature, an electron-deficient Pb⁰/Pb²⁺ dual-center-site catalyst can be achieved. The optimized Pb/PbO@C catalyst showed an excellent performance for the electrochemical hydrogenation of 5-hydroxymethylfurfural (HMF) to high value-added 2,5-bis(hydroxymethyl)furan (BHMF), with high Faradaic efficiency (FE: 91.9%) and selectivity (Sel: 89.7%), achieving comparable performance to those of the reported noble metal-based electrocatalysts. Mechanism study revealed that the electron-deficient Pb⁰/Pb²⁺ dual-center-site provided abundant Lewis acidic sites and promoted the dissociation of water to the active hydrogen (H*) species, thus enhancing the adsorption of HMF on Pb²⁺ sites and the coverage of H* species on Pb⁰ sites. The high coverage of H* species and the synergistic effect of dual-center sites substantially promoted the binding of H* and HMF to form H-HMF* and inhibited the recombination of H* species, thereby accelerating the reaction kinetics of HMF reduction.