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Polymer materials offer controllable structure-dependent performances in separation, catalysis and drug release. Their molecular structures can be precisely tailored to accept Li+ for energy storage applications. Here the design of sp2 carbon-based polyphenylene (PPH) with high lithium-ion uptakes and long-term stability is reported. Linear-PPH (L-PPH) exceeds the performance of crosslink-PPH (C-PPH), due to the fact that it has an ordered lamellar structure, promoting the Li+ intercalation/deintercalation channel. The L-PPH cell shows a clear charge and discharge plateau at 0.35 and 0.15 V vs. Li+/Li, respectively, which is absent in the C-PPH cell. The Li+ storage capacity of L-PPH is five times that of the C-PPH. The reversible storage capacity is further improved to 261 mAh g−1 by functionalizing the L-PPH with the –SO3H groups. In addition, the Li-intercalated structures of C-PPH and L-PPH are investigated via near-edge X-ray absorption fine structure (NEXAFS), suggesting the high reversible Li+ –C C bond interaction at L-PPH. This strategy, based on new insight into sp2 functional groups, is the first step toward a molecular understanding of the structure storage-capacity relationship in sp2 carbon-based polymer.