Surface-enhanced Raman Scattering (SERS) is a rapid and highly sensitive molecular detection technology. Having a highly sensitive and uniform Raman signal is a necessary factor in spectroscopy. Raman substrate structures often face complex processes and high costs. To achieve high-performance SERS, Au-Ag composite nanostructures were prepared by multilayer Au-Ag alternate deposition, annealing and dealloying technology in this research, the method can be used for large-area preparation and facile preparation process. By annealing at a suitable temperature, a large number of nanopores are distributed on the surface of Au-Ag composite nanostructures, which can be firmly distributed on the surface to provide hot spots. The Finite-difference Time-domain (FDTD) method is used to simulate the electric field distribution, and the results show that the Au-Ag composite nanostructure surface can induce great local field enhancement. The experiment results exhibit excellent uniformity and high sensitivity of the SERS detection. The enhancement factor of the Rhodamine 6G (R6G) molecules detected by SERS substrate reaches 2.4×10⁵, and the Relative Standard Deviation (RSD) is as low as 6.9%. The minimum detection concentration of R6G molecules by the Au-Ag composite nanostructures can reach 10⁻¹¹ mol/L. The proposed Au-Ag composite nanostructures and the fabrication process have great potential in preparation of high sensitivity and excellent uniformity SERS substrate.