Organic electrode materials (OEMs) have gathered extensive attention for aqueous zinc‐ion batteries (AZIBs) due to their structural diversity and molecular designability. However, the reported research mainly focuses on the design of the planar configuration of OEMs and does not take into account the important influence of the spatial structure on the electrochemical properties, which seriously hamper the further performance liberation of OEMs. Herein, this work has designed a series of thioether‐linked naphthoquinone‐derived isomers with tunable spatial structures and applied them as the cathodes in AZIBs. The incomplete conjugated structure of the elaborately engineered isomers can guarantee the independence of the redox reaction of active groups, which contributes to the full utilization of active sites and high redox reversibility. In addition, the position isomerization of naphthoquinones on the benzene rings changes the zincophilic activity and redox kinetics of the isomers, signifying the importance of spatial structure on the electrochemical performance. As a result, the 2,2′‐(1,4‐phenylenedithio) bis(1,4‐naphthoquinone) (p‐PNQ) with the smallest steric hindrance and the most independent redox of active sites exhibits a high specific capacity (279 mAh g−1), an outstanding rate capability (167 mAh g−1 at 100 A g−1), and a long‐term cycling lifetime (over 2800 h at 0.05 A g−1).