Flower-like Au nanoparticles, so-called Au nanoflowers (AuNFs), were synthesized by simply adding ascorbic acid to a gold acid solution in the presence of a chitosan biopolymer. The chitosan-entangled AuNFs exhibited strong plasmon absorption in the near-infrared (NIR) wavelength due to the aggregation of primary Au nanoparticles. The chitosan-entangled AuNFs were preferentially adsorbed by Raman-active 2-chlorothiophenol (CTP) molecules, and the CTP-encoded AuNFs (AuNF-CTPs) were subsequently coated with a thin silica layer by a sol-gel reaction with Si alkoxides. The silica-coated AuNFs (AuNF-CTPs@silica) exhibited the distinct Raman signals of adsorbed CTP molecules, as a potential nanoprobe with surface-enhanced Raman scattering (SERS).