A series of molecules based on thienofluorene derivatives as electron donating (D) and benzothiadiazole as electron accepting (A) moieties have been assembled into DAD and ADA architectures in order to investigate the influence of the way of assembling the D and A units along the conjugated backbone, on the photovoltaic performances of bulk heterojunction solar cells. It was found that the major difference in going from ADA to DAD architecture is the change in molecular organization (nematic to crystalline), which increases the charge transport mobility and probably also affects the structural organization in blends with PCBM that ultimately leads to higher photovoltaic performances.