A series of D-A-D type small molecules containing thiophene and benzo[1,2,5]thiadiazole (BT) as electron-donating and electron-accepting units, respectively, were synthesized using palladium-catalyzed Suzuki coupling reactions. The electron-accepting units of BT were modified with pyridyl nitrogen, a single fluorine atom, or two fluorine atoms to enhance their electron-withdrawing abilities, which resulted in DH5TPys, F-DH5TBs, or 2F-DH5TBs, respectively. The solubilizing hexyl groups were introduced at two different beta-positions (3- and 4-positions) on both ends of the thiophene rings. The optical, electrochemical, and photovoltaic properties of the small molecules varied, depending on the introduction of the electron-withdrawing substituents as well as the alkyl variation. The highest occupied molecular orbital (HOMO) energy levels of the small molecules were decreased by the increasing number of fluorine substituents; 4-substitution resulted in deeper HOMO energy levels than 3-substitution. 2F-DH5TB-4 had the lowest HOMO energy level of -5.49 eV. In the organic photovoltaic cells with the configuration ITO/PEDOT:PSS/small molecule:PC71BM/LiF/Al, 2F-DH5TB-4 showed the highest power conversion efficiency (PCE) of 1.11 % owing to the lowest HOMO levels and thus increased the open-circuit voltage. However, two DH5TPys showed low PCEs of 0.20 % despite the deep HOMO energy levels and good UV absorption because of the protonation of pyridyl nitrogen with acidic PEDOT:PSS. In the inverted structure of ITO/ZnO/small molecule:PC71BM/MoO3/Ag, both DH5TPys showed improved PCE values of up to 1.16 %. The device performance of 2F-DH5TB-4 also improved in the inverted structure, showing the PCE of 1.27 %.