To reduce synthetic cost of the classic fluorinated bithienyl benzodithiophene (BDTT-F) unit, here, an alpha-fluorinated bithienyl benzodithiophene unit, namely, α-BDTT-F (F atom in the α position of the lateral thiophene unit), is developed by the isomerization strategy of exchanging the positions of the F atom and flexible alkyl chain on the lateral thiophene unit of the BDTT-F unit. The α-BDTT-F unit was synthesized with less synthetic steps, higher synthetic yield, and less purification times from the same raw materials as those of the BDTT-F unit, thus with low synthetic cost. Theoretical calculation indicates that the α-BDTT-F unit possesses a similar twisted conformation and electronic structures as those of the BDTT-F unit. The α-BDTT-F-based polymer α-PBQ10 exhibits similar light absorption and energy levels as those of the corresponding BDTT-F-based polymer PBQ10 but marginally increased molecular aggregation and stronger hole transport than PBQ10. In consequence, the α-PBQ10:Y6-based polymer solar cell demonstrates a slightly enhanced power conversion efficiency (PCE) of 16.26% compared with that of the PBQ10:Y6-based device (PCE = 16.23%). Also, the PCE is further improved to 16.77% through subtle microscopic morphology regulation of the photoactive layer with the fullerene derivative indene-C60 bisadduct as the third component. This work provides new ideas for the design of low-cost and high-efficiency photovoltaic molecules.