Hierarchical hollow microflowers constructed from mesoporous single crystalline CoMn2O4 nanosheets were synthesized by a solvothermal route followed by calcination in air. It was found that the amount of deionized water plays a key role in the formation of the well-defined hierarchical hollow structure. A possible formation mechanism of the hierarchical hollow microflowers is proposed based on the time-dependent experimental results. In addition, the unique structure of CoMn2O4 microflowers exhibits superior electrochemical performances with an initial discharge specific capacity of 1024 mA h g−1 at 1000 mA g−1 and remains at 650 mA h g−1 with a coulombic efficiency of 98.7% after 500 cycles.