This study establishes the feasibility of bottom-up self-assembly of zero-dimensional graphene oxide quantum dots (GOQDs) into highly ordered, multi-dimensional dendritic nanostructures (F-GOQDs) using a freeze-drying approach. The distinctive features of dendrites have been investigated using various characterization techniques. FT-IR spectroscopy confirmed the presence of carboxyl groups in the dendrite formation mechanism. UV–visible spectroscopy also revealed the oxidation process of graphite sheets, while Raman spectroscopy indicated a slightly lower density of structural imperfections in F-GOQDs than in GOQDs, as evidenced by the ID/IG ratio of 0.97 and 0.93 for GOQDs and F-GOQDs, respectively. The XRD analysis revealed that the crystallite size was 2.3 nm for the GOQDs and 5.5 nm for F-GOQDs. TEM provided insights into the hexagonal particle structure of the GOQDs with a size of 2.25 nm. FESEM and STEM were used to assess the success of the lyophilization process and the form of dendrites, which revealed an average size of 0.6 µm. Dendrite void generation in F-GOQD motifs was investigated at the molecular level using density functional theory (DFT) simulations. The results show that the correlation of the total dipole moment, electrostatic potential, and the decrease in bandgap energy produces these dendrite gaps. Moreover, the wet chemical route employed in this study holds significant potential for the synthesis of both organic and inorganic nanomaterials. The findings of this work not only advance our understanding of dendritic structure and emptiness creation but also offer important guidance for designing and creating novel nanostructures with integrated functionalities.