One of the most effective cost reduction and green engineering projects is to introduce organic compounds to electrode materials instead of expensive inorganic-based materials. In this work, derivatives of perylene diimide substituted with amino acids (PDI_AAs) showed the characteristics of redox-active organic compounds and were, therefore, used as cathode materials of lithium-ion batteries (LIBs). Among the as-synthesized PDI_AAs, the L-alanine-substituted PDI (PDI_A) showed the most improved cycling performances of 86 mAhg−1 over 150 cycles with retention of 95% at 50 mAg−1. Furthermore, at a high current density of 500 mAg−1, PDI_A exhibited a long-term cycling performance of 47 mAhg−1 (retention to 98%) over 5000 cycles. In addition, ex situ attenuated total reflection Fourier-transform infrared spectroscopy (ATR FT-IR) analysis of electrodes at various charging states showed the mechanism of the charge-discharge process of PDI_A.