Three new alternating polymers with the electron-deficient isoindigo group as the acceptor unit and benzo[1,2-b:4,5-b′]dithiophene (BDT) or BDT flanked by thiophenes (or octylthiophenes) as the donor unit were designed and synthesized. All the polymers have good thermal stability, solubility and broad absorption spectra. Their photophysical, electrochemical and photovoltaic (PV) properties were investigated. To understand their different PV performance in the resulting polymer solar cells (PSCs), the morphology of their blends with fullerene derivatives was investigated by atomic force microscopy, and the molecular geometries as well as the molecular frontier orbitals were simulated by density functional theory calculations (Gaussian 09). The polymer PBDT-TIT, with BDT flanked by thiophenes as the donor unit and isoindigo as the acceptor unit, exhibits quite planar backbones and its blend with fullerene derivatives shows optimal morphology. As a result, the PSCs based on PBDT-TIT with a conventional device configuration of ITO/PEDOT:PSS/PBDT-TIT:PC 61BM/LiF/Al showed a power conversion efficiency of 4.22%, with a short-circuit current density of 7.87 mA cm -2, an open-circuit voltage of 0.79 V and a fill factor of 0.68 under the AM 1.5G illumination with an intensity of 100 mW cm -2 from a solar simulator.