Semiconductor superstructures made from assembled and epitaxially connected colloidal nanocrystals (NCs) hold promise for crystalline solids with atomic and nanoscale periodicity, whereby the band structure can be tuned by the geometry. The formation of especially the honeycomb superstructure on a liquid substrate is far from understood and suffers from weak replicability. Here, we introduce 1,4-butanediol as an unreactive substrate component, which is mixed with reactive ethylene glycol to tune for optimal reactivity. It shows us that the honeycomb superlattice has a NC precursor state before oriented attachment occurs, in the form of a self-assembled hexagonal bilayer. We propose that the difference between the formation of the square or honeycomb superstructure occurs during the self-assembly phase. To form a honeycomb superstructure, it is crucial to stabilize the hexagonal bilayer in the presence of solvent-mediated repulsion. In contrast, a square superstructure benefits from the contraction of a hexagonal monolayer due to the absence of a solvent. A second experiment shows the very last stage of the process, where the increasing alignment of NCs is quantified using selected-area electron diffraction (SAED). The combination of transmission electron microscopy (TEM), SAED, and tomography used in these experiments shows that the (100)/(100) facet-to-facet attraction is the main driving force for NC alignment and attachment. These findings are validated by coarse-grained molecular dynamic simulations, where we show that an optimal NC repulsion is crucial to create the honeycomb superstructure.