Highly uniform Cu2S nanocrystals with controllable sizes and shapes (circular and elongated) have been synthesized through a novel water-oil interface confined reaction. They can self-assemble into highly ordered multilayer superlattices. By controlling the size and shape of building block nanocrystals, the packing symmetry of the superlattice can be engineered. For circular nanocrystals, both fcc and hcp multilayer superlattices are found in the sample. For elongated nanocrystals, they can also generate a close-packed layer and further stack into a multilayer superlattice. The dipole moment of the inner nanocrystals is useful for their stacking. This work provides a simple bottom-up approach to integrate nanocrystals, as well as to adjust the packing symmetry of the final superlattice, which may have potential applications for nanomaterials and nanodevices in the future.