Charge transfer is a key phenomenon in the interface of hybrid nanostructure systems. Carbon dots (CDs) display charge transfer characteristics due to their tunable energy level, allowing favorable band alignment with other materials. In this work, it is demonstrated that surface-enhanced Raman scattering (SERS), when combined with other spectroscopic techniques, can provide detailed insights into how carbon-dot-mediated charge transfer enhances the SERS signal of thiolated benzoic acid molecules (TBM) bound to gold nanoparticles (AuNPs). To do this, two different types of carbon dots with different optical properties are used. Additionally, the wavelength-dependent SERS spectral profile shows that charge transfer occurs in the hybrid nanocomposite, which is further proven by the observed fluorescence quenching as well as changes in the average fluorescence lifetime of CDs. It is also found that relative SERS intensity depends on the type of CDs and TBMs, where TBM molecules containing electron withdrawing groups contribute to improvement of SERS signals via charge transfer. This work provides a clear understanding of role of charge transfer process and its role in manipulation of the optical properties of a molecule trapped between AuNP and carbon dots. We believe this sandwich structure opens up new avenues for electronic interface characterization in hybrid nanostructures.