The rational assembly of quantum dots (QDs) in a geometrically well-defined fashion opens up the possibility of accessing the full potential of the material and allows new functions of the assembled QDs to be achieved. In this work, well-confined two-dimensional (2D) and 3D carbon quantum dot (CQD) honeycomb structures have been assembled by electrodeposition of oxygen-rich functional CQDs within the interstitial voids of assemblies of SiO(2) nanospheres, followed by extraction of the SiO(2) cores with HF treatment. Although made from quantum sized carbon dots, the CQD assemblies present a solid porous framework, which can be further used as a sacrificial template for the fabrication of new nanostructures made from other functional materials. Based on the unique honeycomb architecture of the CQDs, which allows the more efficient adsorption of molecules, the formed Au nanoparticles on the CQD honeycomb exhibit 8-11 times stronger surface enhanced Raman scattering (SERS) effect than the widely used Au nanoparticle SERS substrate for the highly sensitive detection of target molecules. This work provides a new approach for the design and fabrication of ultrasensitive SERS platforms for various applications.