Four new D-A polymers PIDTT-Q-p, PIDTT-Q-m, PIDTT-QF-p and PIDTT-QF-m, using indacenodithieno[3,2-b]thiophene (IDTT) as an electron-rich unit and quinoxaline (Q) as an electron-deficient unit, were synthesized via a Pd-catalyzed Stille polymerization. The side chains on the pendant phenyl rings of IDTT were varied from the para- to the meta-position, and the effect of the inclusion of fluorine on the quinoxaline unit was simultaneously investigated. The influence on the optical and electrochemical properties, film topography and photovoltaic properties of the four copolymers were thoroughly examined via a range of techniques. The inductively electron-withdrawing properties of the fluorine atoms result in a decrease of the highest occupied molecular orbital (HOMO) energy levels. The effect of meta-substitution on the PIDTT-Q-m polymer leads to good solubility and in turn higher molecular weight. More importantly, it exhibits optimal morphological properties in the PIDTT-Q-m/PC71BM blends. As a result, the corresponding solar cells (ITO/PEDOT:PSS/polymer:PC71BM/LiF/Al) attain the best power conversion efficiency (PCE) of 6.8%. The structure-property correlations demonstrate that the meta-alkyl-phenyl substituted IDTT unit is a promising building block for efficient organic photovoltaic materials. This result also extends our strategy with regards to side chain isomerism of IDTT-based copolymers for enhanced photovoltaic performance.