GO nanomeshes and [email protected]2/AuNPs nanostructures are formed on the flexible 3D Ni foam substrate for the SERS application. Smaller and denser AuNPs “hot spots” are spin-coated on such mesh-like [email protected]2/AuNPs nanostructures to form AuNPs/[email protected]2/AuNPs SERS substrates. The branches of GO nanomeshes are used as the homogeneous nanogaps to form the separated denser “hot spots” and absorb the molecules, resulting high electromagnetic (confirmed by the FDTD simulation) and signals enhancement. As low as 10−14 M of the Crystal Violet (CV) and Rhodamine 6 G (R6 G) are detected. Such flexible foam-like substrate can be used for the in-situ detection on the fish surface by scraping. DNA without label can also be easily detected by spin-coating the mixed AuNPs-DNA solution in our experiment.