Hotspots have a locally enhanced electromagnetic field, effectively created by nanogaps in plasmonic metal nanostructures. The formation of uniform nanogaps, smaller than a few nanometers, allows for the detection of analytes at low concentrations and ensures reliable measurements across entire surface-enhanced Raman scattering (SERS) substrates. Despite the demand for SERS substrates in recent optical sensing applications, challenges remain in developing new techniques to maximize the number and optimize the size of nanogaps on large-area substrates. To address this issue, this study introduces a new ball-in-hole technique based on metal nanoarchitecture utilizing 3D nanoporous gold film (NPGF) and 0D gold nanoparticles (AuNPs). Using the ball-in-hole technique, 23 nm AuNPs are placed within the ∼ 28 nm mesopores of the metal film, creating uniform nanogaps of just a few nanometers that ensure consistent SERS signals across a large substrate area due to effective hotspots. The 23nmNP@NPGF substrate exhibited an enhancement factor (EF) of 1014 for 4-aminophenol (4-ATP), enabling detection at the attomole level. Moreover, the substrate retained its performance after five washing and reuse cycles, demonstrating excellent recyclability Finally, the substrate successfully detected femtomolar concentrations of key neurotransmitters like dopamine and glutamate, without requiring Raman reporters. This study presents a promising strategy for constructing metal nanoarchitectures with numerous hotspots, offering new possibilities for developing more efficient SERS substrates.