The mechanistic understanding of the intrinsic molecular self-assembly of conjugated polymers is of immense importance to controlling the microstructure development in organic semiconducting thin films, with meaningful impact on charge transport and optoelectronic properties. Yet, to date the vast majority of studies have focused on the fast solution process itself, with studies of slower intrinsic molecular self-assembly in formulations lagging behind. Here we have investigated molecular self-assembly during spontaneous organization and uncovered how changes in formulation influence the microstructure, morphology and transport properties of conjugated polymer thin films. Our results suggest that the polymer-solvent interaction is the key factor for the molecular self-assembly and changes in macroscopic charge transport, which is in contrast with most solution processes, such as spin-coating and blade coating, where solvent drying kinetics dominates the aggregation and crystallization processes. Energetically favourable interactions between the polymer and its solvent are shown to cause chain expansion, resulting in a large hydrodynamic volume and few chain entanglements in solution. This provides molecular freedom for self-assembly and is shown to greatly enhance the local and long range order of the polymer, intra-chain backbone planarity and crystallite size. These improvements, in turn, are shown to endow the conjugated polymer with high carrier transport, as demonstrated by organic thin film transistors.