A two-dimensional flexible surface-enhanced Raman scattering (SERS) filter substrate provides an alternative strategy for the highly sensitive portable detection of various toxic molecules and biomaterials. Herein, we developed a solid-liquid interfacial reduction reaction to post-engineer a solid Au nanostructure surface on filter paper to improve the SERS effect. Among four reductants (ascorbic acid, l-dopamine, hydroquinone (HQ), and formaldehyde), HQ possessed a larger oxidation overpotential and facilitated homogeneous growth, forming small Au branch-structure nanoparticles from HAuCl4 solution. Due to the surface effect by exposing abundant -OH groups and intrinsic aromatic rings from TNA/HQ on nano-gold, the SERS effect on positively charged analytes near the plasmonic Au surface was enhanced, while forming a protective layer against severe water interruption. The resulting SERS substrate with branched nano-gold provided several SERS-enhanced sites, increased the enhancement by more than 6 times compared to original SERS sensing, and displayed a 1.4-7.4 × 105 analytical enhancement factor, which leads to a limit of detection down to several ppb. Less than 6% of deviation in the SERS intensity at different sensing sites was observed. We successfully improved the primary SERS substrate using a high overpotential reductant. Owing to its soft and flexible properties, the paper-based SERS substrate can be used conveniently in different sizes, pasting on curved materials, detecting additives in fish, and preventing the coffee-ring effect, showing high practicality and potential commercial value in the future.