Catalysts prepared through biosynthesis have aroused wide concern recently, but the detailed role of biomolecules and the identification of the main components have not been figured out yet. In this study, biogenic Pd/MgO catalysts were prepared through sol-immobilization (SI) and absorption-reduction (AR) methods, respectively, using Artocarpus heterophyllus Lam leaves extracts as reductant and stabilizer. The catalyst prepared by SI method showed obviously higher benzaldehyde selectivity than that by AR method under the same conditions. The difference can be attributed to the different oxidation behaviors of phenolic hydroxyls between the two synthetic procedures. In the SI procedure, the phenolic hydroxyls were oxidized to semiquinone, while in the AR procedure, the phenolic hydroxyls were oxidized to hydroxyquinone, resulting in less carboxyls binding onto the surface of the Pd nanoparticles (NPs), thus inhibiting the formation of the byproducts. Moreover, gallic acid, chlorgenic acid, and rutin were identified as the most active ingredients in the Artocarpus heterophyllus Lam leaves extracts. Similar catalytic performances were achieved when the model solution containing the three components was used instead of the original plant extracts. The biogenic Pd/MgO-SI catalyst also showed superior stability toward the oxidation of benzyl alcohol.