Four squaraine derivatives SQ, DISQ, MeSQ and DIMeSQ with different substitution indole modifications were synthesized through condensation reaction. Squaraine derivative is one kind of D-AD configuration dyes, which is formed by connecting squaraine with two electron-rich groups through conjugation. The squaraine derivatives were characterized by 1 H NMR, 13 C NMR and high resolution mass spectrometry. The photophysical properties of these squaraine derivatives were studied, such as UV-visible absorption, fluorescence emission, fluorescence quantum yield, fluorescence lifetimes, singlet oxygen quantum yields, and so on. The results showed that, SQ, DISQ, MeSQ and DIMeSQ showed stronger absorption band at 600~700 nm and emission band at 620~800 nm in dichloromethane, which were in near-infrared filed. These four squaraine derivatives were used for singlet oxygen generation, and the highest singlet oxygen quantum yield (6%) was observed for DISQ, which is twice as high as that of DIMeSQ (3%). It is proposed that iodine-substituted and N-hydrogensubstituted molecules are more conducive to intersystem crossing than N-methyl substituted molecules. In addition, It is confirmed that the intramolecular N-H…O force is beneficial to the intersystem crossing of molecules by combining single crystal structure and theoretical calculations. It showed that DISQ could be used as a potential drug for photodynamic therapy.