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Motif‐designed peptide molecules have the unique property to form filamentous nanostructure and the ability to conjugate with other nanoscale building blocks such as graphene and nanoparticles to create functional nanomaterials. Here, the design of a novel functional peptide molecule is reported, which has the abilities to form peptide nanofibers (PNFs) and recognize with graphene quantum dots (GQDs) and graphene oxide (GO) nanosheet specifically. Based on the design of peptide sequence, the ternary GQD‐PNF‐GO nanohybrids are synthesized successfully. The created ternary GQD‐PNF‐GO nanohybrids are characterized by transmission electron microscopy and atomic force microscopy (AFM). To understand the formation mechanism of this ternary nanostructure, the interactions between GQD, PNF, and GO are further investigated by AFM‐based force spectroscopy. Moreover, it is found that the …