In the current emerging sustainable organic battery field, quinones are seen as one of the prime candidates for application in rechargeable battery electrodes. Recently, C6Cl4O2, a modified quinone, has been proposed as a high voltage organic cathode. However, the sodium insertion mechanism behind the cell reaction remained unclear due to the nescience of the right crystal structure. Here, the framework of the density functional theory (DFT) together with an evolutionary algorithm was employed to elucidate the crystal structures of the compounds NaxC6Cl4O2 (x = 0.5, 1.0, 1.5 and 2). Along with the usefulness of PBE functional to reflect the experimental potential, also the importance of the hybrid functional to divulge the hidden theoretical capacity is evaluated. We showed that the experimentally observed lower specific capacity is a result of the great stabilization of the intermediate phase Na1.5C6Cl4O2. The calculated activation barriers for the ionic hops are 0.68, 0.40, and 0.31 eV, respectively, for NaC6Cl4O2, Na1.5C6Cl4O2, and Na2C6Cl4O2. These results indicate that the kinetic process must not be a limiting factor upon Na insertion. Finally, the correct prediction of the specific capacity has confirmed that the theoretical strategy used, employing evolutionary simulations together with the hybrid functional framework, can rightly model the thermodynamic process in organic electrode compounds. (Graph Presented). © 2017 American Chemical Society.