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Optimization of charge generation in polymer blends is crucial for the fabrication of highly efficient polymer solar cells. While the impacts of the polymer chemical structure, energy alignment, and interface on charge generation have been well studied, not much is known about the impact of polymer aggregation on charge generation. Here, we studied the impact of aggregation on charge generation using transient absorption spectroscopy, neutron scattering, and atomic force microscopy. Our measurements indicate that the 1,8-diiodooctane additive can change the aggregation behavior of poly(benzodithiophene-alt-dithienyl difluorobenzotriazole (PBnDT-FTAZ) and phenyl-C61-butyric acid methyl ester (PCBM)polymer blends and impact the charge generation process. Our observations show that the charge generation can be optimized by tuning the aggregation in polymer blends, which can be beneficial for the design of highly efficient fullerene-based organic photovoltaic devices.