Display omitted •GNRs coated with the dual polymer is attractive for cancer therapy.•This is the first report on CS/F-GNRs as novel agents for photothermal therapy.•CS/F-GNRs under laser irradiation could completely ablate tumor in mice.•CS/F-GNRs as safe and highly efficient NIR photothermal agents for cancer therapy. Photothermal therapy (PTT) using chitosan/fucoidan multilayer coating of gold nanorods (CS/F-GNRs) has emerged as an alternative strategy for cancer therapy. In this study, biocompatible CS/F-GNRs were synthesized as a new generation of photothermal therapeutic agents for in vivo cancer treatments owing to their good biocompatibility, photostability, and strong absorption in the near-infrared (NIR) region. The CS/F-GNRs showed a good size distribution (51.87 ± 3.03 nm), and the temperature variation of the CS/F-GNRs increased by 54.4 °C after laser irradiation (1.0 W/cm2) for 5 min. The in vitro photothermal efficiency of CS/F-GNRs indicated that significantly more cancer cells were killed under laser irradiation at 1.0 W/cm2 for 5 min. On the 20th day of treatment, the MDA-MB-231 tumor cells in mice treated with CS/F-GNRs under laser irradiation had almost completely disappeared. Therefore, the biocompatible CS/F-GNRs have shown great promise as safe and highly efficient near-infrared photothermal agents for future cancer therapy.