We successfully synthesized nanoflower-like δ-MnO2, rod-shaped MnOOH, nano-small granular Mn3O4, and the cuboidal and spindle shaped MnCO3 via a facile one-pot hydrothermal method by adjusting the concentration of two sorts of short-chain surfactants with special catechol structures (3-Hydroxytyramine hydrochloride (DA) and 3,4-dihydroxybenzenepropanoic acid (DHCA)) in KMnO4 solution. The XRD and FTIR data demonstrated that the crystal form, morphology and size of the crystal were controlled by small molecule ligands. Afterwards, the relationship between manganese oxides and electrochemical properties was further explored. The results illustrated that nanoflower-like δ-MnO2 with layer structures have the highest specific capacitance of 307.4 F g−1 at a scan rate of 5 mV s−1.