A “sphere plus plate”-composed Au/Ag nanostructure arrays with strong surface-enhanced Raman scattering (SERS) activity are fabricated through the templated method, and the SERS spectrum of polychlorinated biphenyl-77(PCB-77) based on this nanostructure is investigated. The results indicate that the characteristic Raman-shift peaks of PCB-77 may be observed with the bare SERS substrate, but the signal-to-noise ratio of SERS spectrum is too low. By functionalization-modifying decanethiol (DT) on the surface of the bare SERS substrate with the help of the interaction between the -SH group of DT and novel metals, the SERS spectrum of PCB-77 is obviously improved. With the optimal functionalization-modified SERS substrate which is soaked in the DT solution for 36 h, the characteristic Raman-shift peaks’ intensity of the SERS spectrum of PCB-77 gets enhanced greatly.