Embedding isomer entities onto crystalline frameworks with precisely defined spatial distributions represents a promising approach to enhancing the efficiency of oxygen reduction reaction (ORR) in fuel cells. However, accurately constructing covalent organic frameworks (COFs) to regulate energy state effectively remains a significant challenge. Herein, an innovative geometric isomerization strategy aimed at minimizing the rotational barrier energy (ΔE), average local ionization energy (ALIE), and Gibbs free energy (ΔG) for ORR within COFs is proposed. Based on this strategy, isomeric Py-COF-αα with 2,2-substitution, Py-COF-ββ with 3,3-substitution, and Py-COF-αβ with 2,3-substitution on the mainchain frameworks have been obtained. The electronic states and intermediate adsorption capabilities are finely tuned through isomer modification, yielding a precisely controllable chemical activity. Notably, Py-COF-αβ with lower ΔE between thiophenes achieves remarkable performance, evidenced by a half-wave potential of 0.77 V vs reversible hydrogen electrode (RHE), surpassing most reported metal-free electrocatalysts. Combined with theoretical prediction and in situ Raman spectra, it is revealed that the increased dipole moment and non-uniform charge distribution caused by isomer endows pentacyclic-carbon (thiophene β-position) far from sulfur atoms with efficient catalytic activity. This work has opened up a novel paradigm for the isomerization of COFs and underscores the pivotal role of charge regulation in facilitating efficient catalysis.