Ordered structures of self-assembled block copolymers (BCPs) would be the ideal active-layer candidates for high-performance organic electronics. However, fabrication of such structures from BCPs of conjugated polymers has been very limited due to the strong rod-rod interactions between the conjugated blocks, which inhibit the formation of ordered structures. Here, we developed a novel molecular design of conjugated polymer-based graft copolymers to control the rigidity of the copolymers and to produce a variety of ordered nanostructures. A series of well-defined poly(3-hexylthiophene)-graft-poly(2-vinylpyridine) (P3HT-g-P2VP) copolymers were prepared via controlled polymerization, followed by microwave-assisted click reaction. We observed that controlling the molecular weights (M-n) of the grafted P2VP chains allowed us to regulate the rod-rod interaction of the copolymers systematically, as evidenced by differential scanning calorimetry and X-ray scattering measurements. As the M-n of the grafted P2VP chains increased, the crystallinity of the P3HT block in the copolymers gradually decreased so that the enthalpic interaction between P3HT and P2VP chains became more dominant than the rod-rod interaction of the P3HT moiety. Therefore, we produced thermally annealed, well-ordered nonfibril nanostructures of P3HT-based copolymers, including lamellae, hexagonally packed cylinders, and spheres.