Tuning structures of solution‐state aggregation and aggregation‐mediated assembly pathways of conjugated polymers is crucial for optimizing their solid‐state morphology and charge‐transport property. However, it remains challenging to unravel and control the exact structures of solution aggregates, let alone to modulate assembly pathways in a controlled fashion. Herein, aggregate structures of an isoindigo–bithiophene‐based polymer (PII‐2T) are modulated by tuning selectivity of the solvent toward the side chain versus the backbone, which leads to three distinct assembly pathways: direct crystallization from side‐chain‐associated amorphous aggregates, chiral liquid crystal (LC)‐mediated assembly from semicrystalline aggregates with side‐chain and backbone stacking, and random agglomeration from backbone‐stacked semicrystalline aggregates. Importantly, it is demonstrated that the amorphous solution aggregates, compared with semicrystalline ones, lead to significantly improved alignment and reduced paracrystalline disorder in the solid state due to direct crystallization during the meniscus‐guided coating process. Alignment quantified by the dichroic ratio is enhanced by up to 14‐fold, and the charge‐carrier mobility increases by a maximum of 20‐fold in films printed from amorphous aggregates compared to those from semicrystalline aggregates. This work shows that by tuning the precise structure of solution aggregates, the assembly pathways and the resulting thin‐film morphology and device properties can be drastically tuned.