It is beginning to be widely recognized in the organic photovoltaic community that, although fullerene derivatives are remarkable electron acceptors, their total contribution to the solar cell absorption is not large enough to continue to help move power conversion efficiencies upwards. Furthermore, the fullerene electronic structure in turn constrains the donor electronic structure and shrinks the material subspace available for electron donor and acceptor permutations. Recently, non-fullerene electron acceptors have appeared that can outcompete the fullerene in performance, which is no small feat. However, to make a rational push towards power conversion efficiencies in excess of 15%, we must come to grips with the fact that to date, there exists no detailed understanding of how the chemical structure of a small molecule influences the nanoscale morphology in the thin blend film! Insofar as the phase-separated morphology drastically affects both the charge generation yield and rates of charge transport, it is critical that the connection between chemical structure and hierarchical microstructure is made. We have used a combination of charge transport measurements, resonant elastic X-ray scattering across several X-ray absorption edges, and TEM to elucidate how the molecular π-electron contours affect the nanoscale morphology. Using small molecules with varying degrees of π-connectivity and dimensionality, we have shown that the precise conjugation geometry has a large influence not just on the molecular packing on the Angstrom scale, but also on the phase separation and network formation that this packing induces. Our results have important implications for understanding the elusive link between small-molecule chemical structure and thin film morphology.