A two-step method for preparing Au@polypyrrole-chitosan core-shell nanoparticles (Au @ PPy-CS NPs) was fabricated by in situ polymerization of pyrrole monomer on the surface of Au spheres in chitosan solution. Transmission electron microscopy (TEM) images showed the presence of core-shell structure of nanoparticles. Energy-Dispersive Spectroscopy (EDS) and Fourier transform infrared (FTIR) spectroscopy were adopted to verify the shell is polypyrrole-chitosan. Ultraviolet-visible (UV-vis) and X-ray diffraction (XRD) showed that Au was present in the core-shell nanoparticles. The biocompatibility of Au @ PPy-CS NPs was characterized by in vitro for hemolysis assay and cytotoxicity experiments. Results indicated the Au @ PPy-CS NPs had good blood compatibility and low cytotoxicity. The Au @ PPy-CS NPs we proposed provide a promising platform of blood circulation system for early illness diagnosis and therapy.