Five thieno[3,4-c]pyrrole-4,6-dione (TPD)-terthiophene copolymers, PHT, P1F3HT, P1F1HT, P3F1HT, and PFT, having 0, 25, 50, 75, and 100% of fluorine substituents on the center of terthiophene exhibit a progressive increase of open-circuit voltage (V-OC), short-circuit current density (J(SC)), and hence a power conversion efficiency (PCE) up to 9.68% of PC61 BM-blended copolymer photovoltaics, which is the highest PCE reported for TPD-based polymer solar cells with fullerene derivatives as the electron acceptor. It is evident in atomic force microscopy and transmission electron microscopy studies that the width of copolymer nanofibrils formed in solar cells decreases progressively with the increasing fluorine substituents of the copolymers. A declining solubility, which is attributed to the fluorophobic effect, narrows the nanofibril of copolymers with more fluorine substituents. Grazing incidence wide angle X-ray scattering studies reveal the improved crystallinity of lamellar stacking and pi-pi stacking structures of copolymers with more fluorine substituents. Density functional theory calculation indicates a virtually coplanar conformation of terthiophene units with fluorine substituents. The increasing V-OC is also associated with the increasing fluorine substituents, which lower the highest occupied molecular orbital energy level of the copolymers verified by the electrochemical and photoelectron spectroscopic measurements.