Graphene quantum dots (GQDs) with strong photoluminescence (PL) and chemical modification have attracted tremendous interest for fundamental and applied research owing to their special low-cost production and low toxicity. However, most of the research focused on the GQDs without much targeted design, which limited their applications in specific bio-based fields. Inspired by this fascinating conundrum, we demonstrate GQD-based bio-conjugation. Relying on sedimentation coefficient differences for the density gradient ultracentrifuge (DGU) separation of conjugates with different proteins, ultra-purified conjugates were obtained. We demonstrate the first targeted imaging in both cells and tissue models with single or multi color staining, which shows universality for different kinds of biomolecules.