Conjugated polymer cathodes are promising candidates for next-generation Li-ion batteries, but their practical application is limited by the presence of inactive alkyl side chains that reduce specific capacity. A simple heat-treatment strategy is reported to selectively remove the alkyl side chains of a naphthalenediimide (NDI)-based polymer, P(NDI2OD-T2), an n-type conjugated polymer, resulting in a nearly twofold increase in specific capacity, from 56.3 mAh g−1 (fresh) to 117.0 mAh g−1 (heat-treated). Thermogravimetric analysis and gas chromatography-mass spectrometry confirmed the selective cleavage of alkyl groups at 420 °C without significant degradation of the polymer backbone. The resulting porous architecture, verified by Brunauer–Emmett–Teller and scanning electron microscopy analyses, promoted ion diffusion and enhanced the capacitive contribution to charge storage. Electrochemical measurements revealed that the heat-treated cathode exhibited excellent performance at sub-zero temperatures, attributed to improved ion transport and surface-driven storage mechanisms. In contrast, the fresh electrode retained higher electronic conductivity and superior rate capability at room temperature, due to its preserved crystallinity. These findings provide mechanistic insight into how post-processing can modulate the structure–property relationship of conjugated polymer cathodes and offer a versatile and practical approach toward improving specific capacity in organic electrode materials