Uniform nanoporous CuO mesocrystals are synthesized through a low-temperature hydrothermal strategy. The ordered CuO mesocrystal superstructures are assembled by the adsorption of small n-butylamine molecules, which can be easily removed during the subsequent washing process. The CuO mesocrystals demonstrate excellent electrochemical performance for both lithium storage and supercapacitors as compared with CuO single crystals and polycrystals. Our study reveals the structure-performance relationship among the electrochemical performance, morphology, and crystallography construction, which can guide us to optimize the structure of electrode materials for energy storage system.