It is great challenge and interesting for researchers to fabricate substrates for enhanced Raman and sensor, and assemble some easy-to-synthesize metallic nanomaterials into controllable nanostructures with special morphologies and arrangements, via alternating current (AC) electric field. The Au-Ag alloy nanoparticles (Au-Ag alloy NPs) colloidal suspension with excellent dispersibility synthesized by wet chemical method, and the morphology of the assembly can be well controlled by regulating the frequency of the AC electric field. Au-Ag alloy nanochains array (Au-Ag ANCs) with dense plasmonic "hot spots" is formed when the AC electric field of 4Vpp-30kHz is applied, which is supported by the result of finite element method (FEM) numerical simulation. Experimental results demonstrate that Au-Ag ANCs show excellent SERS activity: Au-Ag ANCs can detect both Rhodamine 6G (Rh6G) and crystal violet (CV) in the magnitude order of 10-10 M, and the Raman peaks intensity and analyte concentration has a strong linear correlation (R2 is 0.99339 and 0.95916, respectively). Besides, the introduction of Au-Ag ANCs makes the Raman spectra intensity of thiram (a pesticide) with a concentration of 30 ppm on the surface of the blank ITO glass significantly enhanced, and it can detect thiram with a concentration as low as 0.03 ppm. In addition, Au-Ag ANCs substrate exhibits great uniformity and stability, so they have considerable application potential in the field of quantitative detection of trace substances.