Due to wide applications of lithium-ion batteries (LIBs), scientists have never stopped pursuing larger-capacity and higher-stability lithium storage materials. To obtain better LIBs, three distinct quinone−two-dimensional (2D) MnO2-pillared structures, i.e., p-benzoquinone (C6H4O2)-2D-MnO2, tetrafluoro-p-benzoquinone (C6F4O2)-2D-MnO2, and tetrachloro-p-benzoquinone (C6Cl4O2)-2D-MnO2 were designed and density functional theory calculations were employed to investigate their performance in lithium storages. The calculated theoretical capacities of C6H4O2-2D-MnO2, C6F4O2-2D-MnO2, and C6Cl4O2-2D-MnO2 are 588, 564, and 542 mAh/g, respectively, which are all 2 times larger than that of the mesoporous MnO2. The electrochemical properties are estimated by the open-circuit voltages, which are calculated from the energies of various lithium concentrations in pillared structures. The voltage data show that the three pillared structures possess excellent characteristics for large-capacity lithium storages. Considering that lithium mobility is vital for cycling performance, the lithium diffusion paths and their energy barriers are computed. The thermal stabilities of three pristine and fully lithium-embedded systems were identified through ab initio molecular dynamics simulations at 300 K. Taken together, these results suggest that quinone−2D-MnO2-pillared structures could be prospective materials for larger and more stable lithium storages. Furthermore, our research confirms the possibility of improving lithium storages by pillar construction and provides a prospect for layered material ameliorations.