Nanoparticle assemblies with long-range packing order and preferred crystallographic orientation of building blocks, i.e., mesocrystals, are of high interest not only because of their unique physical properties but also due to their complex structure and morphogenesis. In this study, faceted mesocrystals have been assembled from the dispersion of truncated cubic-shaped iron oxide nanoparticles stabilized by oleic acid (OA) molecules using the nonsolvent “gas phase diffusion technique” into an organic solvent. The effects of synthesis conditions as well as of the nanoparticle size and shape on the structure and morphogenesis of mesocrystals were examined. The interactions of OA-capped iron oxide nanoparticles with solvent molecules were probed by analytical ultracentrifugation and double difference pair distribution function analysis. It was shown that the structure of the organic shell significantly depends on the nature and polarity of solvent molecules. For the nonpolar solvents, the interaction of the aliphatic chains of OA molecules with the solvent molecules is favorable and the chains extend into the solvent. The solvation shell around the nanoparticles is more extended in nonpolar and more compact in polar solvents. There is a clear trend for more spherical particles to be assembled into the fcc superlattice, whereas less truncated cubes form rhombohedral and tetragonal structures. The observed changes in packing symmetry are reminiscent of structural polymorphism known for “classical” (atomic and molecular) crystals.