Although naphthalene diimide (NDI) and its derivatives have been widely used for organic Li-ion batteries (OLIBs), they are limited by a low lithium uptake capacity and ambiguous lithiation mechanism. Herein, we report two isometric thionated-NDI cathodes (cis-2S and trans-2S) obtained by replacing O with S in the imide groups which improves the battery performance compared with parent NDI (P-NDI). Remarkably, the position of S atoms plays an important role as the potential plateau of cis-2S was 100 mV higher than trans-2S, 256 mV higher than P-NDI, and the capacity of cis-2S was twice than that of trans-2S, four times as P-NDI after 400 cycles. The in situ Raman, X-ray photoelectron spectroscopy (XPS), and DFT calculations revealed that the lithiation process occurs on the less electronegative S atoms. For cis-2S, the electron density on the lithiation sites is lower than trans-2S because of a stronger electron inductive effect. This in turn enhances the redox potential and cycling stability of cis-2S. This contribution provides an additional molecular engineering strategy to develop novel organic cathode materials for high performance OLIBs.