Surface-enhanced Raman Scattering (SERS) is a sensitive and nondestructive technique that provides fingerprint structural information of molecules. Designing and constructing sensitive and stable SERS substrates is of great significance for the application of the technique. In this study, single-layer carbon-based dots (CDs) are used as capping agents to synthesize gold nanoparticles (AuNPs/CDs) and manganese dioxide nanosheets (MnO2/CDs), which are then hybridized through a simple cocentrifugation method. After the hybridization, the monodispersive AuNPs/CDs aggregate obviously into some clusters exhibiting strong SERS activity due to the electromagnetic "hot spots" effect, and the MnO2/CDs also show outstanding SERS activity due to the charge-transfer resonance effect. The obtained nanohybrids (MnO2/CDs/AuNPs) with robust chemical stability combine well with the electromagnetic enhancement of AuNPs/CDs and chemical enhancement of MnO2/CDs, leading to an ultrahigh enhancement factor of 3.9 × 108. Based on the novel SERS substrate, a sensitive and rapid sensing system for the detection of malachite green is developed, with a low detection limit of 1 × 10-9 M. This work provides a valuable model for designing and fabricating high-performance SERS substrates.