Abstract The eco‐friendly processing of conjugated polymer binder for lithium‐ion batteries demands improved polymer solubility by introducing functional moieties, while this strategy will concurrently sacrifice polymer conductivity. Employing the polyfluorene‐based binder poly(2,7‐9,9 (di(oxy‐2,5,8‐trioxadecane))fluorene) (PFO), soluble in water‐ethanol mixtures, a novel approach is presented to solve this trade‐off, which features integration of aqueous solution processing with subsequent controlled thermal‐induced cleavage of solubilizing side chains, to produce hierarchically ordered structures (HOS). The thermal processing can enhance the intermolecular π–π stacking of polyfluorene backbone for better electrochemical performance. Notably, HOS‐PFO demonstrated a substantial 6–7 orders of magnitude enhancement in electronic conductivity, showcasing its potential as a functional binder for lithium‐ion batteries. As an illustration, HOS‐PFO protected SiOx anodes, utilizing in situ side chain decomposition of PFO surrounding SiOx particles after aqueous processing are fabricated. HOS‐PFO contributed to the stable cycling and high‐capacity retention of practical SiOx anodes (3.0 mAh cm−2), without the use of any conducting carbon additives or fluorinated electrolyte additives. It is proposed that this technique represents a universal approach for fabricating electrodes with conjugated polymer binders from aqueous solutions without compromising conductivity.