The introduction of side chains in π-conjugated molecules is a design strategy widely exploited to increase molecular solubility thus improve the processability, while directly influencing the self-assembly and consequently the electrical properties of thin films. Here, a multiscale structural analysis performed by X-ray diffraction, X-ray reflectivity, and atomic force microscopy on thin films of dicyanoperylene molecules decorated with either linear or branched side chains is reported. The substitution with asymmetric branched alkyl chains allows obtaining, upon thermal annealing, field-effect transistors with enhanced transport properties with respect to linear alkyl chains. Branched chains induce molecular disorder during the film growth from solution, effectively favouring 2D morphology. Post-deposition thermal annealing leads to a structural transition towards the bulk-phase for molecules with branched chains, still preserving the 2D morphology and allowing efficient charge transport between crystalline domains. Conversely, molecules with linear chains self-assemble into 3D islands exhibiting the bulk-phase structure. Upon thermal annealing, these 3D islands keep their size constant and no major changes are observed in the organic field effect transistor characteristics. These findings demonstrate that the disorder generated by the asymmetric branched chains when the molecule is physisorbed in thin film can be instrumental for enhancing charge transport via thermal annealing.