Manganese oxides with desired structure are controllably obtained through annealing MnCO3 precursors with required structures. The structures of MnCO3 precursors are determined by a “mesocrystal formation” process in an ionic liquid system of a choline chloride/urea (CU) mixture. Without addition of surfactants, only CU solvent and manganese chloride are needed in the reaction system, in which the CU acts as reaction medium as well as control agent for particle growth. A shape transformation of MnCO3 particles from well-defined rhombohedral mesocrystals to ellipsoidal polycrystal ensembles, and to nanoparticulate aggregates is observed when heating the reaction system for 4h at 120, 150, and 180°C, respectively. With a longer aging time at 120°C, etching and disassembly of MnCO3 mesocrystals happened. The correlation between the microstructure and the underlying formation mechanism is highlighted. Porous and nanowire-like MnOx nanostructures are obtained through a facile thermal conversion process from the diverse MnCO3 precursors, which are demonstrated as effective and efficient adsorbents to remove organic waste (e.g. Congo red) from water. Significantly, the nanowire-like MnOx nanostructures obtained by annealing the MnCO3 mesocrystals at 300°C for 4h can remove about 95% Congo red in waste water at room temperature in only one minute, which is superior to the reported hierarchical hollow nanostructured MnO2.