A novel methodology used to overcome the predominance of pi-pi interactions on the organization of rod-coil copolymer is reported in this paper. We demonstrated changes in the self-assembly morphology of poly(3-hexylthiophene)-b-poly(methyl methacrylate) (P3HT-b-PMMA) block copolymer BCP, by introducing an ionic group to the linking unit between the two blocks. A neutral polymer precursor was synthesized from ethynyl-terminated P3HT and azido-terminated PMMA via Huisgen's 1,3-dipolar cycloaddition. Then two 1,2,3-triazolium-based block copolymers with different counteranions were obtained by a quaternization of 1,2,3-triazole groups with methyl iodide, and subsequent anion exchange was observed with a fluorinated salt, bis(trifluoromethane) sulfonimide salt. Atomic force microscopy, modulated differential scanning calorimetry, and X-ray scattering were used to prove that the crystallization of the conjugated block is disrupted by the additional ionic interactions imposed to the system. The 1,2,3-triazolium-based BCP with iodide as the counterion exhibited highly organized well-defined fibrils, as the diblock phase segregation chi becomes predominant over the rod-rod interaction mu. When the more stable and larger NTf2- was used as counterion, P3HT phase was disrupted and no crystallization was observed. This methodology could be a useful strategy to open the range of nanomorphologies reachable with a semiconducting polymer for electronic or photovoltaic applications.