Conjugated copolymers based on isoindigo/fluorinated isoindigo and bis(dialkylthienyl)benzodithiophene, PBDTT-ID and PBDTT-FID, were designed and synthesized for organic photovoltaic applications. The isoindigo fluorination made PBDTT-FID show high PCE of 5.52% and 7.04% in its conventional and inverted PSCs, respectively.