Organic photovoltaic (OPV) cells have drawn increasing attention for decades due to the advantages of low cost, flexibility, lightweight, solution processability, and potential applications in large area devices. The development of new materials, nanomorphological control and device design has led to significantly improved solar cell efficiency up to 15% up to now. Over the long journey of three decades, many photoactive dyes have been systematically explored in metal(electrode)/dye/transparent oxide electrode (typical PV device stack geometries). One family of these promising dyes are squaraine (SQ) dyes which have a typical squaraic bone with four carbon atoms centered in their respective molecules. They are notable for their exceptionally high absorption coefficients extending from the green to the near-infrared. However, the theoretical understanding from molecular level remains challenging in terms of functional group modulation such as diphenylamnino and dissobutylamine groups. Based on experimental results, it shows that SQ donor molecules with diphenylamnino groups has Fill Factor (FF) has high as 0.73 compared with only 0.63 for SQ molecules with dissobutylamine groups. In this work, we use the first-principles simulation to gain a molecular understanding of the close correlation between structure and property. Furthermore, multiple physical parameters have been systemically calculated such as frontier orbitals, light-absorbing capacities, exciton binding energies, intramolecular charge transfer (ICT) properties of SQ, and the exciton dissociation rates at the interface of SQ and C60. The results show that the two functional groups affect the performance of the cells by changing the charge distribution inside the SQ molecules and the separation process of excitons at the interface. The results indicate that the functional group modulation is an effective strategy to enhance the performance of small molecular weight organic thin film solar cells.