A novel alternating polymer, poly{[N-9′-heptadecyl-2,7-carbazole]-alt-5,5-[5′,8′-di-2-thienyl-(6′-fluoro-2′,3′-bis-(3′′-octyloxyphenyl)-quinoxaline)]} (PCzFTQx), based on mono-fluorinated quinoxaline derivative and 2,7-carbazole was synthesized and applied as electron donor material in polymer solar cells. Compared to the corresponding counterpart polymer without fluorine substituent (PCzTQx), PCzFTQx possesses similar absorption properties and optical bandgap (∼2.0 eV). However, the highest occupied molecular orbital (HOMO) energy level of PCzFTQx was lowered to −5.31 eV, about 0.09 eV deeper than that of PCzTQx. Benefit from the low-lying HOMO energy level caused by the strong electron deficient fluorine atom on the quinoxaline unit, the optimized photovoltaic device based on PCzFTQx and phenyl-C₇₁-butyric acid methyl ester (PC₇₁BM) exhibited an enhanced power conversion efficiency (PCE) of 5.19% with corresponding high open-circuit voltage (V_oc) of 0.94 V, relatively to those of 4.72% and 0.82 V for PCzTQx-based device. The experimental data indicated that fluorinated quinoxaline based polymer PCzFTQx should be a promising donor for polymer solar cells.