Aqueous Zn-ion batteries (ZIBs) are very attractive owing to their high safety and low cost. Among various cathode materials, organic materials-based electrodes incorporating various redox functional groups have gained significant attention in the field of ZIBs due to their benefits of a tunable structural design, facility, eco-friendly, and possibility of multivalent energy storage. Herein, we demonstrate the nanostructured organic active materials deposited onto the CNT networks (HyPT@ CNT) for flexible ZIBs. This HyPT nanorods were obtained reassemblying the herringbone structured 3,4,9,10-tetracarboxylic dianhydride through a hydrothermal process in the presence of acid. These HyPT@CNT hybrids were electronically conductive and redox active, as well as could be fabricated into a flexible electrode achieving flexibility from mechanical integrity of robust networked structure. The as-fabricated flexible ZIBs delivered the high capacity of 100 Ah g− 1 at a current density of 0.1 A g− 1 and long-term cycling performance exceeding 5000 cycles. Consequently, these electrochemical performances are associated with the redox reactivity of carbonyl groups as verified by spectroscopic and electrochemical characterizations and the hybridization of HyPT nanorods with CNT networks.