Superlattices of nanoparticles have recently received great attention due to their applications as photonic crystals and templates for ordered nanostructures. So far, only rigid nanoparticles such as inorganic nanocrystals and polymeric latex particles have been considered as materials for superlattices. Block copolymers (BCPs) with weak polyelectrolyte blocks are known to assemble into BCMs, and, depending on the nature of their surface charge, different BCMs may further assemble into higher-order structures. We herein report the self-assemblies of polystyrene-block-poly(acrylic acid) (PS-b-PAA) and polystyrene-block-poly(vinyl pyridine) (PS-b-PVP) in the pH range where the polyelectrolyte blocks of respective BCPs assume opposite charges. By mixing these charge-tuned BCMs, we obtained binary micellar complexes showing the strong crystalline behavior and assigned their crystal structures with small-angle neutron scattering and other analytical techniques. We furthermore demonstrate multiple phases of these binary micellar crystals by varying the size and the charge of BCMs involved. The dependence of the size ratio of individual phases is proven to be different from that of rigid nanoparticles. We believe that such deviation arises from the soft nature of BCMs which can be readily deformed upon swelling in a good solvent. Additionally, thickness and grafting density of the charged shell of each BCM can be altered by varying the respective block lengths, which also allows for the control of their association kinetics. These binary superlattices, constructed from deformable and finely tunable BCMs, has the potential to be applied to materials design such as novel nanostructures and metamaterials.