The fabrication of large-area and flexible nanostructures currently presents various challenges related to the special requirements for 3D multilayer nanostructures, ultrasmall nanogaps, and size-controlled nanomeshes. To overcome these rigorous challenges, a simple method for fabricating wafer-scale, ultrasmall nanogaps on a flexible substrate using a temperature above the glass transition temperature (Tg) of the substrate and by layer-by-layer nanoimprinting is proposed here. The size of the nanogaps can be easily controlled by adjusting the pressure, heating time, and heating temperature. In addition, 3D multilayer nanostructures and nanocomposites with 2, 3, 5, 7, and 20 layers were fabricated using this method. The fabricated nanogaps with sizes ranging from approximately 1 to 40 nm were observed via high-resolution transmission electron microscopy (HRTEM). The multilayered nanostructures were evaluated using focused ion beam (FIB) technology. Compared with conventional methods, our method could not only easily control the size of the nanogaps on the flexible large-area substrate but could also achieve fast, simple, and cost-effective fabrication of 3D multilayer nanostructures and nanocomposites without any post-treatment. Moreover, a transparent electrode and nanoheater were fabricated and evaluated. Finally, surface-enhanced Raman scattering substrates with different nanogaps were evaluated using rhodamine 6G. In conclusion, it is believed that the proposed method can solve the problems related to the high requirements of nanofabrication and can be applied in the detection of small molecules and for manufacturing flexible electronics and soft actuators.