Aqueous manganese-based energy storage systems offer high safety, low cost, and relatively high theoretical capacity, making them promising candidates for large-scale energy storage. However, owing to the strong hydration of multivalent ions, intense electrostatic interactions, and the multiple accessible valence states of manganese oxides, their electrochemical storage processes are jointly governed by electron-lattice coupling, charge transfer across solid-liquid interfaces, and non-equilibrium transport in porous electrodes. From a physics perspective, this review focuses on three key issues: the Jahn-Teller distortion associated with the orbital degeneracy of high-spin Mn³⁺ and its consequences for lattice stability and structural evolution; the regulation of Zn²⁺ desolvation and charge-transfer barriers by interfacial polarization fields, local charge distributions, and solvation structures; and the coupled mechanisms of electrochemical activation, dissolution-deposition, phase reconstruction, and ion-transport limitations in high mass loading electrodes. These processes are integrated into a multiscale framework linking orbital occupation and local lattice strain to interfacial kinetics and macroscopic electrode transport. On this basis, the roles of multi-potential-step measurements, in situ spectroscopy, electrochemical impedance spectroscopy, and physics-based modeling in extracting kinetic parameters and identifying reaction pathways are summarized. The analysis further indicates that optimizing aqueous manganese-based energy storage requires coordinated regulation of Mn valence states, lattice stability, interfacial solvation structures, and coupled electron/ion transport, rather than isolated improvement of a single performance metric. Finally, future challenges involving correlated multivalent-ion transport, operation over a wide temperature range, and interfacial stability under practically relevant conditions are discussed, with the aim of advancing the fundamental understanding and rational design of aqueous manganese-based energy-storage systems.