Mg-based materials are thought to be promising candidates for future hydrogen storage applications due to the low cost, abundant resources and large hydrogen storage capacity. However, they suffer from the challenges of sluggish kinetics and large volume change after hydriding/dehydriding (H/D) process. In order to address the problems, we successfully synthesized the Mg-based Body-Centered Cubic (BCC) metastable nano alloys with much improved kinetics while almost no obvious structure change after H/D process. In this work, the obtained MgCo metastable alloy with BCC structure can reach a hydrogen storage capacity of 3.24 wt% (hydrogen per metal or H/M = 1.28, H/Mg = 2.33) at −15 °C and this absorption temperature in Mg-based BCC structure is the lowest temperature reported for Mg-based materials to absorb hydrogen. Importantly, the BCC structure is maintained without obvious metal lattice change after H/D process. Nevertheless, the potential uptake of about 20 wt% theoretical hydrogen capacity (H/M = 9) for this unique BCC structure cannot be reached up to now. Herein, we discuss the mechanism from the geometrical effect aspect to figure out the difference between the experimental hydrogen storage capacity (H/M = 1.28) and the theoretical one (H/M = 9).