Efficient energy storage devices, i.e. pseudocapacitors, are being intensively pursued to address the environmental and energy crises. Most high-performance pseudocapacitors are based on inorganic materials, while organic materials with broader synthetic tunability have attracted increasing interest. Despite recent progress, electron-deficient (n-type) organic pseudocapacitive materials for flexible energy storage are highly demanded yet remain largely unexplored. Here a novel set of n-type perylene diimide (PDI) based conjugated microporous polymers (CMPs), namely, CMP-1, CMP-2 and CMP-3, have been created to integrate excellent desirable characteristics as organic pseudocapacitor electrode materials for flexible energy storage. In light of electron-accepting redox-active sites, hierarchically porous structures, as well as amide-linked networks, the PDI-CMPs electrodes displayed n-type pseudocapacitive behaviors with high capacity (139–205 F g−1 at 0.5 A g−1), wide and negative biases (−1.0 to 0 V vs. Ag/AgCl), and long cycling stability. CMP-3 consisting of tetraphenylmethane three-dimensional (3D) building block and PDI units demonstrates not only higher capacitance but also better performance stability because of the higher specific surface area and faster diffusion kinetics as compared to its counterpart CMP-1. Asymmetric supercapacitors (SCs) based on CMP-3 and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT/PSS) exhibited wider potential window (1.8 V) and higher capacitance (17.4 mF cm−2) compared with symmetric SCs based on PEDOT/PSS electrodes. Notably, CMP-3 also demonstrates attractive potentials as anode for rechargeable Li-ion batteries. The study sheds light on the fundamental understanding of the key structural parameters that determine their electrochemical and transport properties, thus opening a new door for the rational design of efficient and stable n-type organic electrode materials for flexible energy storage applications.