The development of a water oxidation catalyst has been a demanding challenge in realizing water splitting systems. The asymmetric geometry and flexible ligation of the biological Mn4CaO5 cluster are important properties for the function of photosystem II, and these properties can be applied to the design of new inorganic water oxidation catalysts. We identified a new crystal structure, Mn3(PO4)2·3H2O, that precipitates spontaneously in aqueous solution at room temperature and demonstrated its high catalytic performance under neutral conditions. The bulky phosphate polyhedron induces a less-ordered Mn geometry in Mn3(PO4)2·3H2O. Computational analysis indicated that the structural flexibility in Mn3(PO4)2·3H2O could stabilize the Jahn-Teller-distorted Mn(III) and thus facilitate Mn(II) oxidation. This study provides valuable insights into the interplay between atomic structure and catalytic activity.