Multicomponent nanocrystal assemblies have received great attention due to their fundamental role in the study of self-assembly and novel physical properties arising from particle interactions. Here, we report the formation of the first binary nanocrystal superlattices (BNSLs) consisting of different-sized Fe3O4 nanocrystals. We establish a framework to systematically study the structure of BNSLs using a dual-axis tomography TEM holder. The tilt series obtained not only allows us to map the three-dimensional (3D) structure of icosahdedral AB(13) (ico-AB(13)) and AlB(2)-type BNSLs but also uncovers the structural differences among the projections of ico-AB(13), cuboctahedral AB(13) (cub-AB(13)), and AlB(2). This structural characterization method is general and is important for further exploration of structural diversity in BNSLs and in the development of rigorous structure-property relationships in BNSLs. The formation of ico-AB(13) and AlB(2) BNSLs from electrostatically neutral Fe3O4 nanoparticles is consistent with the space-filling principles and further supports entropy as the dominant factor during the growth of these BNSLs.