Herein, we describe the synthesis of fluorinated polythienothiophene-co-benzodithiophenes (PTBFs) and the characterization of their physical properties, especially their performance in solar cells. Fluorination of the polymer backbone lowered both the HOMO and LUMO energy levels and simultaneously widened the energy bandgap of the polymer (0.1-0.2 eV). Incorporation of fluorine into the various positions of the polymer backbone significantly affected the solar cells' power conversion efficiency from 2.3% to 7.2%. Detailed studies revealed that the polymer containing mono-fluorinated thienothiophene gave the best solar cell performance. Perfluorination of the polymer backbone led to poor compatibility with PC71BM molecules, thus poor solar energy conversion efficiency. This is possibly due to the enhanced self-organization properties of the polymer chains and the fluorophobicity effect. Furthermore, it was found that perfluorination of the polymer backbone resulted in poor photochemical stability against singlet oxygen attack. Theoretical studies indicated that the internal polarization caused enhancement of the negative charge density on thienothiophene rings, which rendered them vulnerable to [2+4] cycloaddition reaction with singlet oxygen.