The invention relates to a one-dimensional chainlike Au-Ag core-shell nanostructure, a self-assembly preparing method and SERS application. Nanoparticles of an Au core and Ag shell structure are synthesized through a liquid-phase synthesis method and a seed crystal growth method; the obtained nanoparticles of the core and shell structure are dispersed in a mixed solution of inorganic salt and ethyl alcohol; a certain quantity of alkaline solution is taken, and the mixed solution is added to be stirred and centrifuged to obtain the one-dimensional chainlike structure. By controlling the electrostatic mutual acting force between the core-shell nanoparticles, the one-dimensional nanometer structure of different Au core sizes and different Ag shell thicknesses is obtained through self-assembly; the method does not need the aid of any templates or surface active agents, the assembly process is simple, the Au core sizes and shell thicknesses are easy to regulate and control, products are easy to separate, the surface Raman enhancing effect of organic substance molecules is remarkable, a preparation system is green and environmentally friendly, no toxic or harmful solvent is added, prepared products are stable in performance, preparation cost is low, the application range is wide, repeatability is high, and large-scale preparation is easy.