In this study, a carbon dots-genipin covalent conjugate (CDs–GP) was synthesized, characterized by Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM), and fluorescence spectroscopy (FL). These carbon dots displayed three dimensional spherical structures with uniform diameters, blue fluorescence (excitation/emission maxima at 355/455 nm), and high water dispersion with a zeta potential of +17.1 mV. Moreover, the CDs–GP conjugate showed excellent biocompatibility with HeLa and A549 cells. Furthermore, the blood compatibility of CDs–GP was evaluated by hemolysis, and hemolysis rates were less than 5%. We deem that combining the outstanding properties of GP with CDs could further promote the development of CDs in biological applications, achieving multifunctional CDs with targeting, in vivo imaging and therapeutic-delivery capabilities. Our in vitro results demonstrated the high uptake of the CDs–GP by cells. Significantly, the prepared CDs–GP exhibited strong optical absorbance under 635 nm laser irradiation, thus the present research demonstrated that the prepared CDs–GP could be employed as a near infrared (NIR)-absorbing agent as well as a non-toxic drug carrier, realizing the synergistic treatment of photothermal therapy (PTT) and drug delivery. The release of heparin (Hep) could be selectively stimulated by NIR-light and low pH, enabling intracellular drug accumulation and thereby enhancing the efficiency. Overall, all these data suggest that the CDs–GP conjugate has a potential application as a drug delivery system and PTT agent.