Ionic self-assembled (ISA) surfactant complexes present a facile concept for self-assembly of various functional materials. However, no general scheme has been shown to allow their overall alignment beyond local polydomain-like order. Here we demonstrate that ionic complexes forming a columnar liquid-crystalline phase in bulk can be aligned within polymer blends upon shearing, taken that the matrix polymers have sufficiently high molecular weight. We use an ISA complex of N,N′-bis(ethylenetrimethylammonium)perylenediimide/bis(2-ethylhexyl) phosphate (Pery-BEHP) blended with different molecular weight polystyrenes (PS). Based on X-ray scattering studies and transmission electron microscopy the pure Pery-BEHP complex was found to form a two-dimensional oblique columnar phase where the perylene units stack within the columns. Blending the complex with PS lead to high aspect ratio Pery-BEHP aggregates with lateral dimension in the mesoscale, having internal columnar liquid-crystalline order similar to the pure Pery-BEHP complex. When the Pery-BEHP/PS blend was subjected to a shear flow field, the alignment of perylenes can be achieved but requires sufficiently high molecular weight of the polystyrene matrix. The concept also suggests a simple route for macroscopically aligned nanocomposites with conjugated columnar liquid-crystalline functional additives.