Graphene quantum dots (GQD) are potential nanomaterials finding applications in various fields. The photoluminescent decay and thermal oxidation properties of GQD reduce its stability and cause inconsistent physicochemical properties. To overcome these limitations, GQD is integrated with zinc oxide quantum dots via a hydrothermal route to produce a graphene-zinc oxide quantum dot (G-ZnO QD) nanocomposite with enhanced stability. The characterization results confirm the formation of G–ZnO quantum dots, while the photoluminescence analysis indicates an improvement in their stability. G-ZnO QD hybrid nanofluids (0.02 wt% to 0.12 wt%), having excellent dispersion stability at neutral pH (zeta potential = −43.5 mV), were prepared. The G-ZnO QD nanofluid exhibits Newtonian behavior and maintains consistent thermal properties for 15 days. A maximum thermal conductivity enhancement of 33% was achieved for 0.12 wt% hybrid nanofluid. Heat transfer experiments by using nanofluid as coolant in a chevron brazed plate heat exchanger demonstrates better performance compared to water. The maximum enhancements of 73.96% in heat transfer coefficient and 38% in Nusselt number were obtained compared to base fluid. The optimal concentration for G-ZnO QD nanofluid was concluded to be 0.1 wt% based on a balance between the enhanced thermal performances and increased pumping power requirements (4% compared to water). These findings highlight that integrating GQD with a suitable metal oxide quantum dot can enhance its stability and thermal properties. G-ZnO QD nanofluids open a new way for future research in next-generation heat transfer and thermal management applications.