A pair of 9-arylidene-9H-fluorene and benzothiadiazole based, low-bandgap copolymers differing merely in the para or meta substitution of alkoxy groups to the arylidene linkages, i.e. p-PAFDTBT and m-PAFDTBT respectively, were comparatively investigated by using morphological characterization, ultrafast spectroscopy and quantum chemical calculations. Despite the subtle difference in the alkoxy substitution patterns, p-PAFDTBT molecules in photoactive films were shown to have a higher degree of crystallinity owing to the relatively less rotational torsion of the arylidene linkages. As a result, in either neat or fullerene-blended films, p-PAFDTBT compared to m-PAFDTBT gave rise to a substantially higher charge yield and much slower charge recombination. This work demonstrates that the alkoxy substitution pattern and the arylidene linkage are highly influencing on the morphology of the photoactive layers and thereby on the photovoltaic performance of the semiconducting copolymers.