Integration of surface-enhanced Raman scattering (SERS) sensors onto transparent and flexible substrates enables lightweight and deformable SERS sensors which can be wrapped or swabbed on various nonplanar surfaces for the efficient collection and detection of analytes on various surfaces. However, the development of transparent and flexible SERS substrates with high sensitivity is still challenging. Here, we demonstrate a transparent and flexible SERS substrate with high sensitivity based on a polydimethylsiloxane (PDMS) film embedded with gold nanostar (GNS) assemblies. The flexible SERS substrates enable conformal coverage on arbitrary surfaces, and the optical transparency allows light interaction with the underlying contact surface, thereby providing highly sensitive detection of analytes adsorbed on arbitrary metallic and dielectric surfaces which otherwise do not provide any noticeable Raman signals of analytes. In particular, when the flexible SERS substrates are covered onto metallic surfaces, the SERS enhancement is greatly improved because of the additional plasmon couplings between GNS and metal film. We achieve the detection capability of a trace amount of benzenethiol (10-8 M) and enormous SERS enhancement factor (∼1.9 × 108) for flexible SERS substrates on Ag film. In addition, because of the embedded structure of GNS monolayers within the PDMS film, SERS sensors maintain the high sensitivity even after mechanical deformations of stretching, bending, and torsion for 100 cycles. The transparent and flexible SERS substrates introduced in this study are applicable to various SERS sensing applications on nonplanar surfaces, which are not achievable for hard SERS substrates.