To meet the requirement of Raman probes (labels) for biocompatible applications, a synthetic approach has been developed to sandwich the Raman-probe (malachite green isothiocyanate, MGITC) molecules between the gold core and the silica shell in gold-SiO₂ composite nanoparticles. The gold-MGITC-SiO₂ sandwiched structure not only prevents the Raman probe from leaking out but also improves the solubility of the nanoparticles in organic solvents and in aqueous solutions even with high ionic strength. To amplify the Raman signal, three types of core, gold nanospheres, nanorods and nanostars, have been chosen as the substrates of the Raman probe. The effect of the core shape on the surface-enhanced Raman scattering (SERS) has been investigated. The colloidal nanostars showed the highest SERS enhancement factor while the nanospheres possessed the lowest SERS activity under excitation with 532 and 785 nm lasers. Three-dimensional finite-difference time domain (FDTD) simulation showed significant differences in the local electromagnetic field distributions surrounding the nanospheres, nanorods, and nanostars, which were induced by the localized surface plasmon resonance (LSPR). The electromagnetic field was enhanced remarkably around the two ends of the nanorods and around the sharp tips of the nanostars. This local electromagnetic enhancement made the dominant contribution to the SERS enhancement. Both the experiments and the simulation revealed the order nanostars > nanorods > nanospheres in terms of the enhancement factor. Finally, the biological application of the nanostar-MGITC-SiO₂ nanoparticles has been demonstrated in the monitoring of DNA hybridization. In short, the gold–MGITC-SiO₂ sandwiched nanoparticles can be used as a Raman probe that features high sensitivity, good water solubility and stability, low-background fluorescence, and the absence of photobleaching for future biological applications.