Surface-enhanced Raman scattering (SERS) signals strongly rely on the interactions and distance between analyte molecules and metallic nanostructures. In this work, the use of a gold nanoparticle (AuNP)-embedded metal-organic framework was introduced for the highly sensitive SERS detection. The AuNPs were in situ grown and encapsulated within the host matrix of MIL-101 by a solution impregnation strategy. The as-synthesized AuNPs/MIL-101 nanocomposites combined the localized surface plasmon resonance properties of the gold nanoparticles and the high adsorption capability of metal-organic framework, making them highly sensitive SERS substrates by effectively preconcentrating analytes in close proximity to the electromagnetic fields at the SERS-active metal surface. We discussed the fabrication, physical characterization, and SERS activity of our novel substrates by measuring the Raman signals of a variety of model analytes. The SERS substrate was found to be highly sensitive, robust, and amiable to several different target analytes. A SERS detection limit of 41.75 and 0.54 fmol for Rhodamine 6G and benzadine, respectively, was demonstrated. The substrate also showed high stability and reproducibility, as well as molecular sieving effect thanks to the protective shell of the metal-organic framework. Subsequently, the potential practical application of the novel SERS substrate was evaluated by quantitative analysis of organic pollutant p-phenylenediamine in environmental water and tumor marker alpha-fetoprotein in human serum. The method showed good linearity between 1.0 and 100.0 ng/mL for p-phenylenediamine and 1.0-130.0 ng/mL for alpha-fetoprotein with the correlation coefficients of 0.9950 and -0.9938, respectively. The recoveries ranged from 80.5% to 114.7% for p-phenylenediamine in environmental water and 79.3% to 107.3% for alpha-fetoprotein in human serum. These results foresee promising application of the novel metal-organic framework based composites as sensitive SERS-active substrates in both environmental and clinical samples.