Herein, two isoindigo-based small molecules, isoindigo (Me-IIG) and thienoisoindigo (Me-TIIG), were synthesized and evaluated as a cathode material in lithium-organic batteries. In a Li coin cell, Me-IIG and Me-TIIG electrode exhibited specific capacity of 156 and 168 mAh g-1 at 1C, corresponding to 84% and 95% of capacity utilization, respectively. The Me-TIIG with better planar molecular geometry than the Me-IIG showed much lower solubility in organic electrolytes with the aid of strong intra- and intermolecular interactions. As a result, the Me-TIIG electrode presented remarkably improved cycling stability, retaining 96% of the initial capacity after 500 cycles at 5C rate. Moreover, Me-TIIG exhibited lower reorganization energy than Me-IIG, which can facilitate a kinetically faster electrochemical pathway, leading to superior rate capability. It should be noted that the Me-TIIG electrode showed excellent rate performance achieving 70% capacity retention at a high rate of 20C.