The spatial configuration of molecules on metal surfaces is a key parameter in reliably modulating the surface-enhanced Raman scattering (SERS) signals quantitatively, but the methods and platforms for controlling this configuration are not well established. Here, we utilized metal-organic frameworks (MOFs) to periodically and spatially arrange molecules in synthesizing zeolite imidazole framework-8 (ZIF-8)/Au core/shell nanocubes (ZACS NCs) for quantitative SERS. The uniform plasmonic Au nanoshell deposition onto ZIF-8 NCs was accomplished by the (100) facets of ZIF-8 and the use of cetyltrimethylammonium chloride (CTAC). In ZACS NCs, an interfacial Au/Zn alloy layer is between the AuNC core and ZIF-8 shell, which can modulate the plasmonic properties of the ZACS NCs. Single-particle Raman analysis suggests that characteristic vibrational Raman moieties of 2-methylimidazole (2-mIM) ligands have a clear laser polarization angle dependence. Importantly, the micro-Raman analysis results from all of the eight different vibrational moieties of ZIF-8 display highly linear relationships between particle concentration and SERS intensity, verifying that the spatially aligned configuration and periodicity of these moieties within ZIF-8 generate quantitative SERS signals. Finally, it was shown that the characteristic Raman peaks of 2-mIM ligands from the ZACS NCs can be used to detect and differentiate various targets of interest. This opens a new paradigm for versatile plasmonic porous materials.