In this research, four new conjugated Bodipy (boron dipyrromethene) structures absorbing in the near IR region have been synthesized and their photophysical, electrochemical, morphological properties and their potential for organic photovoltaics (OPV) have been investigated. All the compounds were substituted with bithiophene units in their 3-and 5-positions. Besides, the meso (8-) and 2-, 6-positions were substituted with different groups, and it allowed analysis of substitution effects in these positions on the performance of organic photovoltaics. Among the synthesized compounds, BTT has better photovoltaic performance than others with 1.3% power conversion efficiency (PCE) value when an organic solar cell with PC71BM acceptor compound was formed under the optimized conditions. Experimental and theoretical studies demonstrated that photovoltaic performance is largely affected by the units on the meso position under the compounds studied and the electronic distributions of the frontier molecular orbitals which are presumably dictated by the orientation of the side groups around the Bodipy core. We believe, with the light of the studies performed novel substitution transformations would enhance implementation of these types of compounds in near infrared photovoltaics.