Herein, a novel strategy to overcome the influence of pi-pi stacking on the rod-coil copolymer organization is reported. A diblock copolymer poly(3-hexylthiophene)-block-poly(ethylene glycol methyl ether methacrylate) (P3HT-b-PEGMA) was synthesized by the Huisgen cycloaddition, so-called "click chemistry", combining the PEGMA and P3HT blocks synthesized by atom transfer radical polymerization and Kumada catalyst transfer polymerization, respectively. Using a dip -coating process, we controlled the original film organization of the diblock copolymer by the crystallization of the P3HT block via pi-pi stacking. The morphology of the P3HT-b-PEGMA films was influenced by the incorporation of gold nanoparticles (GNPs) coated by poly(ethylene glycol) ligands. Indeed, the crystalline structuration of the P3HT sequence was counterbalanced by the addition in the film of gold nanoparticles finely localized within the copolymer PEGMA matrix. Transmission electron microscopy and time -of-flight secondary ion mass spectrometry analysis validated the GNP homogeneous localization into the compatible PEGMA phase. Differential scanning calorimetry showed the rod block crystallization disruption. A morphological transition of the selfassembly is observed by atomic force microscopy from P3HT fibrils into out-of-plane cylinders driven by the nanophase segregation.