A molecular design strategy to achieve highly balanced ambipolar charge transport for donor–acceptor (D–A) isoindigo (IIG)-based copolymer through systematic selection of fluorination positions is reported. To study fluorine substitution site effects on electronic and structural properties, two fluorinated IIG-based copolymers (PIIG-iFT2 and PIIG-oFT2) are synthesized, which contain two fluorine atoms at the bithiophene (T2) inner and outer site and compare them with a nonfluorinated copolymer of IIG and T2 (PIIG-T2) as the reference polymer. Fluorination at the outer site of T2 in PIIG-oFT2 polymer effectively lowers molecular energy levels and increases molecular planarity more than fluorination at the T2 inner site. PIIG-oFT2 organic field-effect transistors show highly balanced ambipolar mobility, hole mobility (μh)/electron mobility (μe) = 1 by increasing electron mobility, whereas PIIG-T2 (μh/μe = 9.0) and PIIG-iFT2 (μh/μe = 2.4) exhibit unbalanced ambipolar transport. The ambipolar complementary-like inverter is also demonstrated by simple one-time coating of PIIG-oFT2 with gain = 21.