Hydroxyapatite (HAP) materials are widely applied as biomedical materials due to their stable performance, low cost, good biocompatibility and biodegradability. Here, a green, fast and efficient strategy was designed to construct a fluorescent nanosystem for cell imaging and drug delivery based on polyethyleneimine (PEI) and functionalized HAP via simple physical adsorption. First, HAP nanorods were functionalized with riboflavin sodium phosphate (HE) to provide them with fluorescence properties based on ligand-exchange process. Next, PEI was attached on the surface of HE-functionalized HAP (HAP-HE@PEI) via electrostatic attraction. The fluorescent HAP-HE@PEI nanosystem could be rapidly taken up by NIH-3T3 fibroblast cells and successfully applied to for cell imaging. Additionally, doxorubicin hydrochloride (DOX) containing HAP-HE@PEI with high loading capacity was prepared, and in-vitro release results show that the maximum release of DOX at pH 5.4 (31.83%) was significantly higher than that at pH 7.2 (9.90%), which can be used as a drug delivery tool for cancer therapy. Finally, HAP-HE@PEI as the 3D inkjet printing ink were printed with GelMA hydrogel, showing a great biocompatible property for 3D cell culture of RAW 264.7 macrophage cells. Altogether, because of the enhanced affinity with the cell membrane of HAP-HE@PEI, this green, fast and efficient strategy may provide a prospective candidate for bio-imaging, drug delivery and bio-printing.