A precise control over the meso- and microstructure of ordered and aligned nanoparticle assemblies, i.e., mesocrystals, is essential in the quest for exploiting the collective material properties for potential applications. In this work, we produced evaporation-induced self-assembled mesocrystals with different mesostructures and crystal habits based on iron oxide nanocubes by varying the nanocube size and shape and by applying magnetic fields. A full 3D characterization of the mesocrystals was performed using image analysis, high-resolution scanning electron microscopy and Grazing Incidence Small Angle X-ray Scattering (GISAXS). This enabled the structural determination of e.g. multi-domain mesocrystals with complex crystal habits and the quantification of interparticle distances with sub-nm precision. Mesocrystals of small nanocubes (l = 8.6-12.6 nm) are isostructural with a body centred tetragonal (bct) lattice whereas assemblies of the largest nanocubes in this study (l = 13.6 nm) additionally form a simple cubic (sc) lattice. The mesocrystal habit can be tuned from a square, hexagonal to star-like and pillar shapes depending on the particle size and shape and the strength of the applied magnetic field. Finally, we outline a qualitative phase diagram of the evaporation-induced self-assembled superparamagnetic iron oxide nanocube mesocrystals based on nanocube edge length and magnetic field strength.