Exploration of electrode materials with well-defined nanostructures and good flexibility is an efficient approach for achieving high-performance and flexible energy storage systems. However, it is still challenging to well integrate active materials into flexible electrodes and simultaneously maintain satisfactory electrochemical performance. Herein, we successfully synthesize novel three-dimensional graphene (3DG)-encapsulated porous multishelled NiO hollow microsphere (3DG/pMS-NiO) composite aerogels via a modified self-templating method and a dopamine (DA)-assisted self-assembly route. The well-designed highly interconnected porous 3DG network and the close contact NiO-graphene structure of the 3DG/pMS-NiO composite aerogels offer multiple advantages such as high porosity and accessible area, improved conductivity, enhanced electrolyte diffusion and a simple electrode preparation process. Thus, the as-prepared flexible 3DG/pMS-NiO electrodes showed significantly improved specific capacitance of 710.4 F g-1 at 0.5 A g-1 and excellent rate capability with an ultrahigh capacitance retention of 92.5% at 10 A g-1. In addition, the fabricated asymmetric supercapacitors (3DG/pMS-NiO//AC) showed a high specific capacitance of 34.4 F g-1 at 1 A g-1 with a voltage window of 0-1.6 V, a large energy density of 12.3 W h kg-1 at a power density of 815.3 W kg-1, and a decent cycling stability. This work profoundly enlightens the material design and electrode preparation, and even opens up an avenue for the development of high-performance and flexible energy storage systems.