We report a highly ordered intercalated hexagonal binary superlattice of hydrophilically functionalized single-walled carbon nanotubes (p-SWNTs) and surfactant (C₁₂E₅) cylindrical micelles. When p-SWNTs (with a diameter slightly larger than that of the C₁₂E₅ cylinders) were added to the hexagonally packed C₁₂E₅ cylindrical-micellar system, p-SWNTs positioned themselves in such a way that the free-volume entropies for both p-SWNTs and C₁₂E₅ cylinders were maximized, thus resulting in the intercalated hexagonal binary superlattice. In this binary superlattice, a hexagonal array of p-SWNTs is embedded in a honeycomb lattice of C₁₂E₅ cylinders. The intercalated hexagonal binary superlattice can be highly aligned in one direction by an oscillatory shear field and remains aligned after the shear is removed.