Solution-phase conformations and charge photogeneration dynamics of a pair of low-bandgap copolymers based on benzo[1,2-b:4,5-b(')]dithiophene (BDT) and thieno[3,4-b]thiophene (TT), differed by the respective carbonyl (-C) and ester (-E) substituents at the TT units, were comparatively investigated by using near-infrared time-resolved absorption (TA) spectroscopy at 25 °C and 120 °C. Steady-state and TA spectroscopic results corroborated by quantum chemical analyses prove that both PBDTTT-C and PBDTTT-E in chlorobenzene solutions are self-aggregated; however, the former bears a relatively higher packing order. Specifically, PBDTTT-C aggregates with more π-π stacked domains, whereas PBDTTT-E does with more random coils interacting strongly at the chain intersections. At 25 °C, the copolymers exhibit comparable exciton lifetimes (~1 ns) and fluorescence quantum yields (~2%), but distinctly different charge photogeneration dynamics: PBDTTT-C on photoexcitation gives rise to a branching ratio of charge separated (CS) over charge transfer (CT) states more than 20% higher than PBDTTT-E does, correlating with their photovoltaic performance. Temperature and excitation-wavelength dependent exciton∕charge dynamics suggest that the CT states localize at the chain intersections that are survivable up to 120 °C, and that the excitons and the CS states inhabit the stretched strands and the also thermally robust orderly stacked domains. The stable self-aggregation structures and the associated primary charge dynamics of the PBDTTT copolymers in solutions are suggested to impact intimately on the morphologies and the charge photogeneration efficiency of the solid-state photoactive layers.