The invention provides a graphene coated nano silver array flexible surface enhanced Raman substrate material which consists of three parts, namely a flexible filtering membrane, a nano silver array assembled on the surface of the flexile filtering membrane, and graphene coating the surface of the nano silver array. The invention further provides a preparation method and application of the material as a surface enhanced Raman substrate. The graphene coated nano silver array flexible surface enhanced Raman substrate material provided by the invention has good Raman enhancement effects and excellent chemical stability, and meanwhile is convenient in sampling and testing. Therefore, graphene coated nano silver array which is provided by the invention and is high in stability and uniform in large size can be used as a surface enhanced Raman substrate for high-sensitivity rapid detection on trace toxic organic chemicals, biomarkers and pathogenic bacteria or viruses.