Recently, battery-type electrode materials, such as transition metal oxides/molybdates, have attracted extensive attention in the development of high-performance supercapacitors (SCs), owing to their rich redox chemistry, high theoretical capacity and superior electrochemical activity. Herein, we prepared battery-type redox behavior-enabled tricopper dimolybdate (Cu3Mo2O9) with versatile morphologies of nanoflakes (NFs) and nanoparticles (NPs) by a facile hydrothermal method for SCs. With different reactants, the shape of Cu3Mo2O9 was altered under constant growth conditions. The morphological and structural characteristics of the prepared samples were investigated by FE-SEM, XRD and XPS analyses. Moreover, the electrochemical properties of the Cu3Mo2O9 nanostructures were evaluated in 1 M KOH electrolyte. From these results, the Cu3Mo2O9 NF sample exhibited a high areal capacity of 29.6 μAh/cm2 at 1 mA/cm2 with good rate capability of 61.1% at 20 mA/cm2, which are higher compared to the NP sample. Furthermore, the capacity retention of 131.3% (after 2000 cycles) was observed without any capacity fading for the Cu3Mo2O9 NFs, indicating the great cycling durability of the material. Such remarkable durability of the Cu3Mo2O9 nanostructures could be served as an efficient electrode in energy storage devices.