A biofilm is an established assemblage of bacterial communities with an extracellular matrix (ECM), that causes persistent bacterial infections resistant to antimicrobial agents. Developing efficient agents to inhibit bacterial biofilm matrix formation are essential for treatment of chronic, recurrent biofilm infections. Engineered nanoparticles to facilitate antibacterial effect have been investigated to treat biofilm infection. Graphene quantum dots (GQDs) as nano-sized graphene sheets have been investigated for antibacterial application due to its reactive oxygen species production, membrane interaction, as well as their unique properties and biocompatibility. Here we report the discovery that GQDs interrupt formation of amyloid protein fibers, which is responsible for Staphylococcus aureus amyloid biofilm integrity. Experimental and computational results have revealed that GQDs interacted with phenol soluble modulins (PSMs) peptides in the amyloid-like fibers at N-terminal and led to stable conformation of GQD-PSM docking. Such assembly changed the secondary structure of the peptides, as a result, inhibited /delayed the amyloid fiber formation. In addition, presented data in long term treatment of GQD on PSM fibrillation indicated potential co-assembly of peptides and GQDs into new forms of fibers. We demonstrated anti-biofilm activity of GQDs through interacting with PSM peptides in ECM and co-assembly into new form of amyloid-like fibers. This work revealed the promising potential of GQDs as anti-biofilm agents and potential nano-bionic that can selectively manipulate ECM of bacterial community.