The mesostructure of ordered arrays of anisotropic nanoparticles is controlled by a combination of packing constraints and interparticle interactions, two factors that are strongly dependent on the particle morphology. We have investigated how the degree of truncation of iron oxide nanocubes controls the mesostructure and particle orientation in drop cast mesocrystal arrays. The combination of grazing incidence small-angle X-ray scattering and scanning electron microscopy shows that mesocrystals of highly truncated cubic nanoparticles assemble in an fcc-type mesostructure, similar to arrays formed by iron oxide nanospheres, but with a significantly reduced packing density and displaying two different growth orientations. Strong satellite reflections in the GISAXS pattern indicate a commensurate mesoscopic superstructure that is related to stacking faults in mesocrystals of the anisotropic nanocubes. Our results show how subtle variation in shape anisotropy can induce oriented arrangements of nanoparticles of different structures and also create mesoscopic superstructures of larger periodicity.