Both morphology and chemical composition (e.g. fluorination) of charge transfer copolymers impact power conversion efficiency in bulk heterojunction solar cells. Here we used transient absorption spectroscopy to elucidate the impact of these differences on the exciton/charge photogeneration, recombination and dissociation dynamics.We studied the excited state dynamics of singlet excitons, polaron pairs and polarons on weak donor acceptor medium gap copolymers (PBnDT-XTAZ, where X= F or H).These systems have different morphological characteristics depending upon the molecular chemistry and processing solvent, which can be characterized by absorption spectra with different aggregation behavior. J- and H-aggregated materials show different optical cross section strengths for their 0-0 and 0-1vibronic transitions due to difference in the intrachain and interchain electronic coupling. Initial excitations on different aggregation systems lead to difference in the branching of the emission and dissociation of photoexcited species. H-aggregation leads to formation of more secondary excitations such as polaron pairs whereas J-aggregation leads to more primary excitations (singlet excitons). We found that photoinduced absorption of polaron pairs dominates stimulated emission in H- aggregated PBnDT-FTAZ film as compared to J aggregated PBnDT-FTAZ and PBnDT-HTAZ. In addition, the photoinduced absorption of singlet excitons, probed at 0.95 eV, shows the slow decay of H-aggregated PBnDT-FTAZ relative to other two films, indicating retardation in recombination rate in H-aggregated FTAZ. This trend is also consistent with the photoluminescence decay of these three samples. These observations are independent of fluorination but depend strongly on aggregation. However, the polaron absorption band at~1.3 eV depends upon the fluorination but is independent of the aggregation.These differences in the exciton and polaron/polaron pair related dynamics due to morphological and chemical structure variations can impact the photovoltaic performance of the bulk heterojunction made from these polymers.