We designed and synthesized a novel series of two-dimensional (2D) conjugated polymers (P1-2T, P2-2T2F and P3-4T2F) containing 2,2′-bithiophene (2T) and 3,3′-difluoro-2,2′-bithiophene (2T2F) as donor units, and 4,7-benzo[c][1,2,5]thiadiazole (BT) and 4,7-di(thiophen-2-yl)benzo[c][1,2,5]thiadiazole (DTBT) as acceptor units appended with conjugated vinyl-terthiophene (VTT) side chain. We comprehensively investigated the effect of fluorination and thiophene (T) π-spacer on the optoelectronic properties and photovoltaic performance of the resulting copolymers. In comparison with non-fluorinated polymer P1-2T, the fluorinated polymer P2-2T2F and P3-4T2F had down shifted highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels with an enhanced absorption band. Moreover, 2D grazing incidence wide-angle X-ray scattering and space charge limited current measurement showed that the presence of thiophene π-spacer in P3-4T2F promoted dominant face-on orientation, high crystallinity and enhanced hole mobility, compared with P2-2T2F. As a result, the inverted polymer solar cell based on the P3-4T2F:PC61BM blend exhibited a high power conversion efficiency (PCE) of 6.66% with a Jsc of 12.99 ± 0.30 mA/cm−2. In contrast, the P1-2T:PC61BM and P2-2T2F:PC61BM devices without π-spacer showed a PCE of 2.22% and 0.95%, respectively. The PCE of the P3-4T2F:PC61BM device was further improved to 6.89% by using a polyethylenimine ethoxylated (PEIE) interlayer between ITO and ZnO. This study reinvigorates the key modulation of a 2D conjugated polymer with improved photovoltaic performance.