Being well-known as an excellent sorbent, metal-organic frameworks (MOFs) have been employed to intergrate with noble metal nanoparticles to fabricate active substrates for surface-enhance Raman spectroscopy (SERS) sensing applications. In this work, we employed three organic molecules with different molecular dimensions, including urea, methylene blue (MB) and Congo red (CR) for investigating SERS performance of a ZIP-8/Ag heterostructure. While every dimension of urea is smaller than the pore size of ZIP-8, MB and CR has one dimension larger than that of the pore size. The results show that only urea experienced large SERS enhancements on ZIP-8/Ag sensing platform. In contrast, MB and CR exhibited lower SERS intensity on ZIP-8/Ag than on pure Ag nanoparticle substrates. Adsorption capacities of those analyte were then calculated to confirm that urea could be adsorbed into ZIP-8/Ag at the best rate. The size-dependent mechanism of analyte adsorption and improving SERS signal was then confirmed using two other organic compounds: 4-nitrophenol (4-NP) and chloramphenicol (CAP). Thanks to the size-selective adsorption, small molecules such as urea and 4-NP can be effectively detected in the presence of large interfering molecules, which is useful for developing advanced SERS applications. The ZIP-8/Ag-based SERS sensor could detect urea at impressive concentrations as low as 1.48 × 10