Directing the orientation of anisotropic nanocrystal assemblies is important for harnessing the shape-dependent properties of nanocrystal solids in devices. We control the orientation of smectic B superlattices of CdSe/CdS dot-in-rod nanocrystals through assembly on different polar interfaces and quantify the superlattice orientation through correlated small- and wide-angle grazing-incidence diffraction. Small-angle scattering is used to determine the phase of the nanorod superlattices and their preferential growth directions from the subphase. Wide-angle diffraction is used to quantify the orientations of nanorods within the superlattices and with respect to the substrate. Not only are the nanorod long axes aligned within the structures, but truncation of the short axes also coaligns the crystal axes of the nanorods with the zone axes in assembled smectic B crystals. Three dimensional orientational alignment of nanocrystals in superlattices is highly desirable in device applications. Depending on the subphase used for self-assembly, the films range from nearly quantitative vertical to horizontal alignment. Controlling for other variables, we find that the surface tension of the subphase is strongly correlated with the orientational ordering of the nanorod superlattices. The microstructure of nanorod superlattices shows many classic defects of atomic and liquid crystalline systems. The nature of defect structures supports a mechanism of nuclei formation on the subphase–solvent interface rather than in solution. Last, we demonstrate the relationship between optical absorption polarization and superlattice structure using correlated optical spectroscopy and electron microscopy.