We demonstrated flower-like 3D Ag-Au hetero-nanostructures on an indium tin oxide glass (ITO glass) for surface enhanced Raman scattering (SERS) applications. The flower-like 3D Ag nanostructures were obtained through electrodeposition with liquid crystalline soft template which is simple, controllable and cost effective. The flower-like 3D Ag-Au hetero-nanostructures were further fabricated by galvanic replacement reaction of gold (III) chloride trihydrate (HAuCl4·3H2O) solution and flower-like Ag. The flower-like Ag-Au hetero-nanostructure exhibited stronger SERS effects and better chemical stability compared with flower-like Ag nanostructure. The localized surface plasmon resonance (LSPR) spectra, field emission scanning electron microscope (FESEM) photos and Ag-Au ratios were studied which show that the surface morphology and shape of the flower-like Ag-Au hetero-nanostructure play significant roles in enhancing SERS. The flower-like 3D Ag-Au hetero-nanostructures fabricated by electrodeposition in liquid crystalline template and galvanic replacement reaction are simple, cheap, controllable and chemical stable. It is a good candidate for applications in SERS detection and imaging.