The growing demand for lightweight and flexible supercapacitor devices necessitates innovation in electrode materials and electrode configuration. We have developed a new type of three-dimensional (3D) flexible nanohybrid electrode by incorporating nanoporous polyaniline (PANI) into layer-by-layer ionic liquid (IL) functionalized carbon nanotube (CNT)-graphene paper (GP), and explored its practical application as a freestanding flexible electrode in a supercapacitor. Our results have demonstrated that the surface modification of graphene nanosheets and CNTs by hydrophilic IL molecules makes graphene and CNTs well-dispersed in aqueous solution, and also improves the hydrophility of the assembled graphene-based paper. Furthermore, the integration of highly conductive one-dimensional (1D) CNTs with two-dimensional (2D) graphene nanosheets leads to 3D sandwich-structured nanohybrid paper with abundant interconnected pores, which is preferred for fast mass and electron transport kinetics. For in situ electropolymerization of PANI on paper electrodes, the IL functionalized CNT-GP (IL-CNT-GP) offers large surface area and interlayer spacing and the unique π surface of graphene and CNTs for efficient and stable loading of PANI. A key finding is that the structural integration of multiple components in this 3D freestanding flexible sheet electrode gives rise to a synergic effect, leading to a high capacitance of 725.6 F g(-1) at a current density of 1 A g(-1) and good cycling stability by retaining 90% of the initial specific capacitance after 5000 cycles.