In this study, we report the design of a DNA sensor for the detection of a DNA sequence representative of the hepatitis B virus (HBV) based on a sandwich assay and surface-enhanced Raman scattering (SERS) measurement. The temperature-responsive hybrid silicon substrate was first prepared via immobilization of capture DNA strand at the surface of gold nanoparticles on the hybrid silicon substrate. A sandwich strategy was then applied for the detection of target DNA that brings a reporter DNA labeled with indocyanine green to the proximity of the surface, leading to high SERS signals. The temperature-responsive hybrid silicon substrate-based SERS platform can detect the remarkably lowest HBV DNA concentrations at similar to 0.44fm at 25 degrees C and similar to 0.14fm at 37 degrees C, respectively, which are comparable with the lowest HBV DNA concentration ever via other techniques. We expect this highly sensitive and robust hybrid silicon substrate-based SERS platform can be extended to detect other biomolecules and chemical species such as viruses, proteins, and small molecules without any labeling. Copyright (c) 2017 John Wiley & Sons, Ltd.