Two isomeric small molecule donors, C2-C-F and C2-M-F, with only the different substitution positions of the alkyl chains on the intermediate bridged trithiophene units, were designed and synthesized. It was found that the alkyl chain substitution position has little effect on their absorptions and energy levels, but has a significant impact on the morphology of the active layers when blended with the acceptor BTP-4F-12. Better morphology was obtained for the active layer based on small molecule donor C2-C-F, and an efficiency of 12.84% was achieved for the C2-C-F-based photovoltaic device. This result indicates that the morphology of the active layer can be finely regulated through the alkyl substitution positions, providing a useful avenue for the design of efficient small molecule donors.