Donor–acceptor conjugated polymers based on benzo[1,2-b:5,4-b′]difuran (syn-BDF) or benzo[1,2-b:5,4-b′]difuran (anti-BDF) as donors and isoindigo as acceptors were synthesized by Stille cross-coupling reaction. The effects of syn- and anti-repeating units on optical, electrochemical and photovoltaic properties of polymers were investigated. The anti-PBDFID displayed lower optical bandgap and higher HOMO energy level than syn-PBDFID. The syn-PBDFID had better solubility than anti-PBDFID. The energy levels of two new polymers were compared with some related benzo[1,2-b:4,5-b′]dithiophenes (BDTs) based polymers. The results suggested that the utilization of less conjugated repeating units such as syn-BDF and the elimination of electron donating groups on the central phenyl ring of BDF can effectively lower the HOMO energy level of polymer. The low HOMO energy level of syn-PBDFID enabled high open circuit voltages in PSC devices.