Carbohydrate conjugate rod-coil amphiphiles were synthesized and their self-assembling behavior in aqueous solution was investigated. These amphiphiles were observed to self-assemble into supramolecular structures that differ significantly depending on the molecular architecture. The rod-coil amphiphiles based on a short coil (1) self-assemble into a vesicular structure, while the amphiphiles with a long coil (2) show a spherical micellar structure. In contrast, 3, based on a twin-rod segment, was observed to aggregate into cylindrical micelles with twice the diameter of molecular length scale. As a means to determine the binding activity to protein receptors of these supramolecular objects, hemagglutination inhibition assay was performed. The experiments showed that the supramolecular architecture has a significant effect on the binding activity. In addition, incubation experiments with Escherichia coli showed that mannose-coated objects specifically bind to the bacterial pili of the ORN 178 strain. These results demonstrate that precise control of the nano-objects in shape and size by molecular design can provide control of the biological activities of the supramolecular materials.