Nanostructured manganese oxides (Mn3O4, MnOOH) were successfully prepared by a hydrothermal method using MnCl2 as manganese source, NaOH as precipitation agent and H2O2 as oxidant. The composition and morphology of the products were determined by the dripping speed of NaOH solution, the adding order of reactant and the hydrothermal time. Single phase of Mn3O4 nanoparticles can be prepared by dropwise addition of the NaOH solution to the solution of MnCl2 and H2O2. While single phase of MnOOH nanorods can be obtained by pouring the NaOH solution into the reaction system quickly or changing the adding order of NaOH and H2O2. When the dripping speed of NaOH solution was 6mL/min, and an appropriate amount of surfactant (C18H29NaO3S) was added, Mn3O4 nanorods can be obtained. The hydrothermal method can be readily controlled to synthesize Mn3O4 and MnOOH with different morphologies. The Mn3O4 sample had higher capacitance than the MnOOH sample. The morphologies of these samples had little effect on their electrochemical performance.