5-Hydroxyindole-3-acetic acid (5-HIAA) is a molecular marker that can be used in the early diagnosis of carcinoid tumors, and the development of sophisticated 5-HIAA assays is therefore of great importance. Surface-enhanced Raman spectroscopy (SERS) has been widely used for the rapid and sensitive detection of disease biomarkers. Insufficient specificity for tumor markers and poor spectral reproducibility are the bottlenecks in the practical use of SERS technology. In this study, based on MIL-125 surface-loaded gold nanoparticles (Au@MIL-125), a novel strategy was proposed to obtain Au@MIL-125@molecularly imprinted polymers (MIPs) as functional SERS substrates by wrapping a thin MIP shell around the Au@MIL-125 surface for selective separation followed by a 5-HIAA assay. The Raman peak intensity ratio (I