AbstractSurface enhanced Raman scattering (SERS), as a promising and convenient analytical tool for molecule sensing, has turned out to be one of the most important applications of plasmonic nanostructures. However, its large‐area production, controllability, and adjustability remain significant challenges because of the weak control over the fabrication and spatial arrangement. Herein, a silicon nanogap array‐based flexible plasmonic substrate is developed, with capabilities of large‐area production, controllable arrangement, and width of nanogaps, by utilizing the standard microfabrication platform, and the fabricated flexible plasmonic substrate is further explored for dynamically tunable SERS for molecular sensing. After experimentally and theoretically optimizing the geometric designs of precursors, a 90 × 90 silicon nanogap array (over 1 cm × 1 cm) with a yield of about 99.74% is achieved. SERS is realized by depositing Au films onto the silicon nanogap. Dynamically tunable SERS is demonstrated by the thermally induced local stretch or contraction of silicon nanogaps, where the key parameters including Raman enhancement and sensitivity of the molecular sensor can be conveniently adjusted. These presented results significantly expand the scope of engineering opinions for flexible plasmonic nanostructures, which have many envisioned applications especially for environmental monitoring and biochemical detection.