Use of renewable raw materials for fabrication catalysts with excellent catalytic performance is of considerable importance for sustainable chemistry. Here, biowaste soybean curd residue (SCR) was used to prepare porous N-doped carbon materials (PNCM) via the carbonization method, and subsequently modified with small Pd nanoparticles (NPs) to generate the Pd/PNCM catalyst. Pd/PNCM was used for catalytic hydrogenation of phenol to cyclohexanone, as the latter is an important chemical intermediate that is usually produced under harsh reaction conditions. The Pd/PNCM catalyst can hydrogenate phenol to cyclohexanone in aqueous solution under mild reaction conditions with excellent catalytic performance. In addition, compared to commercial Pd/C, Pd/PNCM exhibits excellent catalytic performance and stability, which is attributed to the synergetic effects of N-doping of porous carbon supports and stabilization of ultra-small Pd NPs. Thus, this study highlights a new pathway for preparing N-doped porous carbon materials using biomass waste as the precursor material, and subsequently fabricating precious metal-modified catalysts with excellent catalytic performance for sustainable and green catalysis.