The rational synthesis of mixed transition metal oxides (MTMOs) with three-dimensional hierarchical porous structure has been proved to be an effective strategy for improving electrochemical performances of binary metal oxides. Herein, the hierarchically Ni1-xMnxCo2O4 nanoflowers are synthesized by a facile hydrothermal method combined with subsequent heat-treatment. It is found that Ni/Mn atom ratio has a significant influence on the microstructures and electrochemical properties of Ni1-xMnxCo2O4. The Ni0.5Mn0.5Co2O4 sample with a Ni/Mn atom ratio of 1 exhibits the highest specific capacity of 366 F/g at a current density of 1 A/g as compared to the other Ni1-xMnxCo2O4 samples. In addition, Ni0.5Mn0.5Co2O4 displays high rate capability and cycling performance. The excellent electrochemical performances of Ni0.5Mn0.5Co2O4 could be ascribed to the large surface area and high mesoporosity, leading to the increased accessible surface for ion access and the rapid electrochemical reactions. The as-synthesized Ni0.5Mn0.5Co2O4 nanoflowers could be used as a potential electrode materials for Supercapacitors. Furthermore, this study provides a facile method to synthesize other MTMOs with three-dimensional hierarchical nanostructure. An asymmetric supercapacitor is assembled with Ni0.5Mn0.5Co2O4 as the positive electrode and activated carbon as the negative electrode. The supercapacitor shows an energy density of 20.2 Wh/kg at a power density of 700 W/kg. Cycling stability is achieved with 82% retention after 5000 charge-discharge cycles.