Achieving efficient polymer solar cells (PSCs) requires a structurally optimal donor-acceptor heterojunction morphology. Here we report the combined experimental and theoretical characterization of a benzodithiophene-benzo-thiadiazole donor polymer series (PBTZF4-R; R = alkyl substituent) blended with the non-fullerene acceptor ITIC-Th and analyze the effects of substituent dimensions on blend morphology, charge transport, carrier dynamics, and PSC metrics. Varying substituent dimensions has a pronounced effect on the blend morphology with a direct link between domain purity, to some extent domain dimensions, and charge generation and collection. The polymer with the smallest alkyl substituent yields the highest PSC power conversion efficiency (PCE, 11%), reflecting relatively small, high-purity domains and possibly benefiting from "matched" donor polymer-small molecule acceptor orientations. The distinctive morphologies arising from the substituents are investigated using molecular dynamics (MD) simulations which reveal that substituent dimensions dictate a well-defined set of polymer conformations, in turn driving chain aggregation and, ultimately, the various film morphologies and mixing with acceptor small molecules. A straightforward energetic parameter explains the experimental polymer domain morphological trends, hence PCE, and suggests strategies for substituent selection to optimize PSC materials morphologies.