The flexible surface-enhanced Raman scattering (SERS) sensor, which has the bionic 3D nanoarray structure of a beetle-wing substrate (BWS), was successfully prepared by replicated technology and thermal evaporation. The bionic structure was replicated with polydimethylsiloxane (PDMS) and then silver (Ag) nanoisland thin films were deposited by thermal evaporation. The deposition times and thicknesses (25–40 nm) of the Ag thin films were manipulated to find the optimal SERS detection capability. The Ag nanoisland arrays on the surface of the bionic replicated PDMS were observed by scanning electron microscope (SEM), X-ray diffraction (XRD), and contact angle, which can generate strong and reproducible three-dimensional hotspots (3D hotspots) to enhance Raman signals. The water pollutant, rhodamine 6G (R6G), was used as a model molecule for SERS detection. The results show that 35 nm Ag deposited on a PDMS-BWS SERS substrate displays the strongest SERS intensity, which is 10 times higher than that of the pristine BWS with 35 nm Ag coating, due to the excellent 3D bionic structure. Our results demonstrate that bionic 3D SERS sensors have the potential to be applied in wearable devices and sensors to detect biomolecules and environmental pollutants, such as industrial wastewater, in the future.