Rechargeable multivalent ion battery such as Mg-ion battery is considered as a candidate for high-density battery technology because of its high volumetric capacity and low tendency to form dendrites. Development of cathode materials for Mg-ion batteries requires good understanding of the intercalation and adsorption processes of Mg²⁺ ions into and on the host materials. We observed recently that nanostructure is beneficial for the development of Mg²⁺ cathode materials with high capacity. In this work, we describe the preparation of flower-like three-dimensional (3D) nanostructures of birnessite MnO₂ through an electrochemical conversion reaction from γ-MnS. This 3D birnessite MnO₂ exhibited a total capacity of ~360 mAh/g in aqueous electrolyte for the initial cycle. We further characterized the insertion of Mg²⁺ ions in the atomic layers of MnO₂ nanoflowers using scanning transmission electron microscopy (STEM) technique, revealing the energy storage mechanism of Mg²⁺ ions in 3D, ion-accessible MnO₂ nanostructures.