Quasi-two-dimensional (2D) fully π–d conjugated metal–organic frameworks (MOFs) have been widely employed as active materials of secondary batteries; however, the origin of their high charge storage capacity is still unknown. Some reports have proposed a mechanism by assuming the formation of multiple radicals on one organic ligand, although there is no firm evidence for such a mechanism, which would run counter to the resonance theory. In this work, we utilized various magnetometric techniques to monitor the formation and concentration of paramagnetic species during the electrochemical process of 2D π–d conjugated Cu-THQ MOF (THQ = tetrahydroxy-1,4-benzoquinone). The spin concentration of the fully reduced (discharged 1.5 V) electrode was estimated to be around only 0.1 spin-1/2 per CuO4 unit, which is much lower than that of the expected “diradical” form. More interestingly, a significant elevation of the temperature-independent paramagnetic term was simultaneously observed, which indicates the presence of delocalized π electrons in this discharged state. Such results were corroborated by first-principles density functional theory calculations and the electrochemically active density of states, which reveal the microscopic mechanism of the charge storage in the Cu-THQ MOF. Hence, a graphite-like charge storage mechanism, where the π-electron band accepts/donates electrons during the charge/discharge process, was suggested to explain the excessive charge storage of Cu-THQ. This graphite-like charge storage mechanism revealed by magnetic studies can be readily generalized to other π–d conjugated MOFs.