Developing electrode materials with high-energy densities is important for the development of lithium-ion batteries. Here, we demonstrate a mesoporous molybdenum dioxide material with abnormal lithium-storage sites, which exhibits a discharge capacity of 1,814 mAh g(-1) for the first cycle, more than twice its theoretical value, and maintains its initial capacity after 50 cycles. Contrary to previous reports, we find that a mechanism for the high and reversible lithium-storage capacity of the mesoporous molybdenum dioxide electrode is not based on a conversion reaction. Insight into the electrochemical results, obtained by in situ X-ray absorption, scanning transmission electron microscopy analysis combined with electron energy loss spectroscopy and computational modelling indicates that the nanoscale pore engineering of this transition metal oxide enables an unexpected electrochemical mass storage reaction mechanism, and may provide a strategy for the design of cation storage materials for battery systems.