We have designed and synthesized two low bandgap conjugated copolymers containing alternating meta-fluoro-p-alkoxyphenyl- (m-FPO-) or p-fluoro-m-alkoxyphenyl- (p-FPO-) substituted benzodithiophenes-co-benzooxadiazole (BO), named PBO-m-FPO and PBO-p-FPO. The properties, including UV-vis absorption, charge mobility and photovoltaic performance of the two polymers have been intensively investigated. The results indicated that the introduction of fluorine atom at m, p positions of phenyl substituted benzodithiophene unit hardly affected their absorption spectra and highest occupied molecular orbital (HOMO) level. However, the two polymers showed different photovoltaic properties. Power conversion efficiencies (PCEs) based on the device structure of ITO/PEDOT:PSS/polymer:PC71BM/Ca/Al demonstrated a large distinction (5.9% for PBO-m-FPO vs 2.8% for PBO-p-FPO) at optimal weight ratio. When replacing the Ca layer with zirconium acetylacetonate (ZrAcac), using 3% 1,8-diiodooctane (DIO) as the active layer additive, the PCEs of PBO-m-FPO and PBO-p-FPO increased by 36% (8.0% vs 5.9%) and 85% (5.1% vs 2.8%), respectively. The active layer's mobilities, morphology and molecular packing resulted in a significant difference in short-circuit current density (J(sc)) and fill factor (FF).