We studied the electronic and structural properties of electron-deficient anthraquinone (AQ) derivatives, Me4N4AQ and TCNAQ, and investigated their charge-discharge properties in lithium ion batteries along with those of AQ. Cyclic voltammogram, X-ray structure analysis and theoretical calculations revealed that these three acceptors have different features, such as different electron-accepting properties with different reduction processes and lithium coordination abilities, and different packing arrangements with different intermolecular interactions. These differences greatly affect the charge-discharge properties of lithium ion batteries that use these compounds as cathode materials. Among these compounds, Me4N4AQ showed a high charge/discharge voltage (2.9–2.5 V) with high cyclability (>65% of the theoretical capacity after 30 cycles; no decrease after 15 cycles). These results provide insight into more in-depth design principles for lithium ion batteries using AQ derivatives as cathodic materials.