Au-Ag alloy nanoparticles with an atomic ratio of 1∶1 were synthesized by using hydrazine as a reducing agent, and the as-prepared nanoparticles were then assembled on silicon substrate. The surfaces of alloy nanoparticles were treated by immersion into a solution of HAuCl4 to dissolve some Ag atoms from the alloy nanoparticles. With pyridine as the probe, the difference in the SERS effect on the alloy nanoparticles was investigated before and after the surface treatment processes. The results revealed that the SERS signals increased initially and then decreased with the immersion time. The time dependence was mainly attributed to the change of surface micro-structures of the alloy nanoparticles. The surface reaction of the Au-Ag nanoparticles with HAuCl4 underwent two processes involving the formation of surface pinhole (dealloying) and the deposition of AgCl(s) on surface. The former promoted the SERS effect, while the latter attenuated the SERS effect.