For further the understanding of the adsorption mechanism of heavy metal ions on the surface of protein-inorganic hybrid nanoflowers, a novel protein-derived hybrid nanoflower was prepared to investigate the adsorption behavior and reveal the function of organic and inorganic parts on the surface of nanoflowers in the adsorption process in this study. Silk fibroin (SF)-derived and copper-based protein-inorganic hybrid nanoflowers of SF@Cu-NFs were prepared through self-assembly. The product was characterized and applied to adsorption of heavy metal ion of Pb(II). With Chinese peony flower-like morphology, the prepared SF@Cu-NFs showed ordered three-dimensional structure and exhibited excellent efficiency for Pb(II) removal. On one hand, the adsorption performance of SF@Cu-HNFs for Pb(II) removal was evaluated through systematical thermodynamic and adsorption kinetics investigation. The good fittings of Langmuir and pseudo-second-order models indicated the monolayer adsorption and high capacity of about 2000 mg g−1 of Pb(II) on SF@Cu-NFs. Meanwhile, the negative values of Δ r G m ( T ) θ and Δ r H m θ proved the spontaneous and exothermic process of Pb(II) adsorption. On the other hand, the adsorption mechanism of SF@Cu-HNFs for Pb(II) removal was revealed with respect to its individual organic and inorganic component. Organic SF protein was designated as responsible ‘stamen’ adsorption site for fast adsorption of Pb(II), which was originated from multiple coordinative interaction by numerous amide groups; inorganic Cu3(PO4)2 crystal was designated as responsible ‘petal’ adsorption site for slow adsorption of Pb(II), which was restricted from weak coordinative interaction by strong ion bond of Cu(II). With only about 10% weight content, SF protein was proven to play a key factor for SF@Cu-HNFs formation and have a significant effect on Pb(II) treatment. By fabricating SF@Cu-HNFs hybrid nanoflowers derived from SF protein, this work not only successfully provides insights on its adsorption performance and interaction mechanism for Pb(II) removal, but also provides a new idea for the preparation of adsorption materials for heavy metal ions in environmental sewage in the future.