IR-780 iodide is a near-infrared (NIR) fluorescence dye with higher and more stable fluorescence intensity than clinically applied dye indocyanine green (ICG). Meanwhile, IR-780 can be utilized in photothermal therapy with laser irradiation. IR-780 is an important theranostic agent but its lipophilicity limited its application. In this paper, we synthesize multifunctional heparin-folic acid-IR-780 nanoparticles (HF-IR-780 NPs) by self-assembly of the heparin-folic acid conjugate and IR-780 through ultrasonic sound method. The HF-IR-780 NPs exhibit good monodispersity, significant stability, and excellent molecular targeting to folate receptor over-expressing MCF-7 cells. Furthermore, the in vivo biodistribution experiments show that the HF-IR-780 NPs are specifically targeted to the tumor and can be used for tumor imaging. The in vitro cell viability assays and in vivo photothermal therapy experiments indicate that MCF-7 cells or MCF-7 xenograft tumors could be ablated by combining HF-IR-780 NPs with irradiation of an 808 nm laser. The photothermal therapy in vivo with a single-dose treatment has not caused significant adverse effect. The resulted HF-IR-780 NPs are a potential theranostic agent for imaging-guided cancer therapy.