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Core-shell nanoparticles are at the leading edge of the hot research topics and offer a wide range of applications in optics, biomedicine, environmental science, materials, catalysis, energy, and so forth, due to their excellent properties such as versatility, tunability, and stability. They have attracted enormous interest attributed to their dramatically tunable physicochemical features. Plasmonic core-shell nanomaterials are extensively used in surface-enhanced vibrational spectroscopies, in particular, surface-enhanced Raman spectroscopy (SERS), due to the unique localized surface plasmon resonance (LSPR) property. This review provides a comprehensive overview of core-shell nanoparticles in the context of fundamental and application aspects of SERS and discusses numerous classes of core-shell nanoparticles with their unique strategies and functions. Further, herein we also introduce the concept of shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) in detail because it overcomes the long-standing limitations of material and morphology generality encountered in traditional SERS. We then explain the SERS-enhancement mechanism with core-shell nanoparticles, as well as three generations of SERS hotspots for surface analysis of materials. To provide a clear view for readers, we summarize various approaches for the synthesis of core-shell nanoparticles and their applications in SERS, such as electrochemistry, bioanalysis, food safety, environmental safety, cultural heritage, materials, catalysis, and energy storage and conversion. Finally, we exemplify about the future developments in new core-shell nanomaterials with different functionalities for SERS and other surface-enhanced spectroscopies.