Fluorinated conjugated polymers leading to enhanced photovoltaic device performance has been widely observed in a variety of donor-acceptor copolymers; however, almost all these polymers have fluorine substituents on the acceptor unit. Building upon our previously reported PBnDT-FTAZ, a fluorinated donor-acceptor conjugated polymer with impressive device performance, we set this study to explore the effect of adding the fluorine substituents onto the flanking thiophene units between the donor unit (BnDT) and the acceptor unit (TAZ). We developed new synthetic approaches to control the position of the fluorination (3′ or 4′) on the thiophene unit, and synthesized four additional PBnDT-TAZ polymers incorporating the fluorine-substituted-thiophene (FT) units, 3′-FT-HTAZ, 4′-FT-HTAZ, 3′-FT-FTAZ, and 4′-FT-FTAZ. We discover that relocating the fluorine substituents from the acceptor to the flanking thiophene units have a negligible impact on the device characteristics (short circuit current, open circuit voltage, and fill factor) when comparing 4′-FT-HTAZ with the original FTAZ. Combining these two fluorination approaches together, 4′-FT-FTAZ shows even higher device performance than FTAZ (7.7% vs 6.6%) with active layers over 200 nm in thickness. Furthermore, high values of fill factor∼70% are all achieved for photovoltaic devices based on 3′-FT-HTAZ, 4′-FT-HTAZ, or 4′-FT-FTAZ, ascribed to the observed high hole mobilities (over 1 × 10-3 cm2/(V s)) in these devices. Our study offers a new approach to utilize the fluorinated thiophene units in developing new conjugated polymers to further improve the device performance of polymer solar cells.