The trinary hydroxyapatite@Fe3O4@N‐doped carbon dots (HA@Fe3O4@N‐CDs) hybrids were prepared by one‐pot hydrothermal approach and utilized to detect and remove lead ion from aqueous solution. The structures and morphologies of as‐obtained nanorod‐like HA@Fe3O4@N‐CDs hybrids were characterized by X‐ray diffraction, scanning electron microscopy, and X‐ray photoelectron spectroscopy measurements. These HA@Fe3O4@N‐CDs hybrids possess good magnetism by magnetic hysteresis test and multi‐colored fluorescence by the CLSM measurement. Furthermore, the as‐obtained hybrids display excellent biocompatibility by MTT assay. Importantly, the trinary magnetic HA@Fe3O4@N‐CDs hybrids as a green detector and adsorbent of Pb2+ were investigated. The influence of the different pH, the concentration of heavy metal, and the maximum adsorption capacity on removal efficiency was measured in detail. The maximum Pb2+ adsorption capacity on HA@Fe3O4@N‐CDs hybrids is 450 mg/g. The kinetic mechanism was a pseudo‐second order model, and the isotherm data was fitted well by the Langmuir isotherm and Freundlich model. Hence, the nanorod‐like HA@Fe3O4@N‐CDs hybrids could be a multifunctional material with significant potential applications in heavy metal detection and adsorption, bone tissue regeneration, magnetic therapy, and biomedicine. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2019.