One of the most challenging issues in developing supercapacitor and capacitive deionization (CDI) technologies is the rational design and synthesis of active electrode materials, with favorable morphologies, reasonable porous structure and high surface area. Recently, three-dimensional (3D) graphene frameworks (3DGF)-based hybrids have been considered as one of the most promising candidates for supercapacitor and CDI applications. By incorporating functional nanomaterials into 3DGF, the obtained 3DGF-based hybrids exhibited enhanced properties or unique character compared to 3DGF. Here we report novel hierarchical hybrids with microporous carbon spheres (MCS) decorated 3DGF (3DGF-MCS), which not only possesses a hierarchical porous structure, but also maintains favorable features for supercapacitor and CDI applications, such as a large surface area and good electrical conductivity. The results indicate that 3DGF-MCS with 10wt% MCS exhibits excellent electrochemical performances, including a superior specific capacitance of 288.77Fg⿿1, and an ultrahigh electrosorption capacity of 19.8mgg⿿1. The 3DGF-MCS should be promising electrode materials for highly efficient supercapacitor and CDI applications.