This study presents a multi-step strategy to enhance the thermoelectric performance of zinc oxide (ZnO) by interfacing lowly-oxidized graphene quantum dots (GQDs) with 3D nanostructured ZnO. The 3D GQD@ZnO heterostructure exhibits a high dimensionless figure-of-merit (zT) value of approximately 0.486 at 580 K, the highest reported for ZnO-based materials. The fabrication process involves creating a highly periodic 3D thin-shell ZnO using proximity field nanopatterning (PnP) and then decorating it with GQDs through a solution process. This approach reduces thermal conductivity by effectively scattering phonons at nanostructured surfaces and grain boundaries, while enhancing the Seebeck coefficient through energy filtering at the GQD/ZnO interface. The interfacial energy barrier of 0.63 eV at the GQD/ZnO interface traps low-energy electrons, improving power factor by 74% compared to bare 3D ZnO. The 3D GQD@ZnO heterostructure shows a significant reduction in thermal conductivity from 1.49 to 0.785 W m⁻¹K⁻¹, leading to an exceptional zT value of 0.486 at 580 K. This work demonstrates that multi-scale nanostructuring techniques can significantly improve the thermoelectric performance of non-traditional materials, opening new possibilities for wearable and flexible thermoelectric devices.This study presents a multi-step strategy to enhance the thermoelectric performance of zinc oxide (ZnO) by interfacing lowly-oxidized graphene quantum dots (GQDs) with 3D nanostructured ZnO. The 3D GQD@ZnO heterostructure exhibits a high dimensionless figure-of-merit (zT) value of approximately 0.486 at 580 K, the highest reported for ZnO-based materials. The fabrication process involves creating a highly periodic 3D thin-shell ZnO using proximity field nanopatterning (PnP) and then decorating it with GQDs through a solution process. This approach reduces thermal conductivity by effectively scattering phonons at nanostructured surfaces and grain boundaries, while enhancing the Seebeck coefficient through energy filtering at the GQD/ZnO interface. The interfacial energy barrier of 0.63 eV at the GQD/ZnO interface traps low-energy electrons, improving power factor by 74% compared to bare 3D ZnO. The 3D GQD@ZnO heterostructure shows a significant reduction in thermal conductivity from 1.49 to 0.785 W m⁻¹K⁻¹, leading to an exceptional zT value of 0.486 at 580 K. This work demonstrates that multi-scale nanostructuring techniques can significantly improve the thermoelectric performance of non-traditional materials, opening new possibilities for wearable and flexible thermoelectric devices.