Fluorination represents an important strategy in developing high-performance conjugated polymers for photovoltaic applications. Here, we use regioregular poly(3-ethylhexylthiophene) (P3EHT) and poly(3-ethylhexyl-4-fluorothiophene) (F-P3EHT) as simplified model materials, using single-molecule/aggregate spectroscopy and molecular dynamic simulations, to elucidate the impacts of backbone fluorination on morphology and excitonic coupling on the molecular scale. Despite its high regioregularity, regioregular P3EHT exhibits a rather broad distribution in polymer chain conformation due to the strong steric hindrance of bulky ethylhexyl side chains. This conformational variability results in disordered interchain morphology even between a few chains, prohibiting long-range effective interchain coupling. In stark contrast, the experimental and molecular dynamic calculations reveal that backbone fluorination of F-P3EHT leads to an extended rod-like single-chain conformation and hence highly ordered interchain packing in aggregates. Surprisingly, the ordered and close interchain packing in F-P3EHT does not lead to strong excitonic coupling between the chains but rather to dominant intrachain excitonic coupling that greatly reduces the molecular energetic heterogeneity.