In this work, we systematically studied the shape- and size-controlled monodisperse synthesis of iron oxide nanocrystals (IONCs) for their use as building blocks in the formation of mesocrystals. For this aim, on understanding the influence of the oleic acid concentration, iron-oleate concentration, and heating rate on the synthesis of robust and reproducible IONCs with desired sizes and shapes, we synthesized highly monodisperse similar to 11 nm sized nanocubes and nanospheres. Magnetic measurements of both cubic and spherical IONCs revealed the presence of mixed paramagnetic and superparamagnetic phases in these nanocrystals. Moreover, we observed that the magnetic moments of the nanocubes are more substantial compared to their spherical counterparts. We then demonstrated a simple magnetic-field-assisted assembly of nanocubes into three-dimensional (3D) cuboid mesocrystals while nanospheres did not form any mesocrystals. These findings indicate that small cubic nanocrystals hold great promise as potential building blocks of 3D magnetic hierarchical structures with their superior magnetic properties and mesocrystal assembly capability, which may have high relevance in various fields ranging from high-density data storage to biomedical applications.