It was of crucial importance to modify perylene-3,4,9,10-tetracarboxylic acid bisimides (PBIs) for the design of new perylene-based bio-dye agents with strong fluorescence. Recently, we reported that ethanolamine (EA)-functionalized poly(glycidyl methacrylate) (or PGEA) can produce good transfection efficiency, while exhibiting very low toxicity. Herein, the low-toxic PGEA was proposed to be conjugated with PBIs via facile atom transfer radical polymerization for the well-defined highly fluorescent cationic bifunctional conjugate (PBI–PGEA). The obtained PBI–PGEA exhibited good water-solubility properties, characteristic spectroscopic patterns of PBIs, and excellent photostability. The PBI–PGEA conjugate can be used as an efficient cell bio-dye for rapid (2–5 min) cell labeling at low concentrations (0.06–0.12 mg mL−1). Such a fast labeling process did not induce obvious cytotoxicity, avoiding possible side-effects to the cells. In addition, the PBI–PGEA still possessed good gene transfection efficiency in different cell lines. With the strong fluorescence in water and good transfection properties, the developed bifunctional PBI–PGEA should possess more potential in bioimaging and gene delivery.