The application of surface-enhanced Raman scattering (SERS) spectroscopy to ultrasensitively and quantitatively analyze small molecules of interest in biological samples has been a challenging endeavor, on account of the signal contamination caused by a variety of macromolecules including lipids, proteins and nucleic acids. Herein, we designed a “three-in-one” multifunctional substrate (Au ETHH@ZIF-8) composed of Au elongated tetrahexahedron (Au ETHH) and zeolitic imidazolate framework-8 (ZIF-8) with analyte enrichment, filtration and enhanced SERS performance for the detection of 4-nitrobenzenethiol (4-NBT). Au ETHH nanocrystals with a high density of sharp edges and tips enhance SERS performance. The ZIF-8 shell with the porous structure surrounding the Au ETHH, allows those analytes of comparable or smaller size to the pore size to reach the surface of the Au ETHH and possesses moderate analyte enrichment property. In addition, the prepared Au ETHH@ZIF-8-based SERS sensor realized the ultrasensitive and quantitative detection of 4-NBT in whole blood.