Based on the intricate pathogenesis of periodontitis and the advantages of mild photothermal therapy (PTT) and nanotherapy, a multifunctional photothermal nanoplatform (designated BR@C3G-Cu) was rationally developed by coating bilirubin nanoparticles (BR NPs) with copper ion coordinated cyanidin-3-O-glucoside metal-polyphenol networks (MPNs) in this study. The synergistic consequences of the photothermal conversion properties and metal-dependent functionality of this MPNs contributed to the effective and persistent elimination of periodontal pathogens under safe and mild conditions, meeting the heterogeneous antibacterial requirements of periodontitis.