Carbon-based three-dimensional (3D) freestanding electrode materials typically possess weak mechanical properties such as brittleness, low stress, residual strain, and large energy dissipation during deformation processes. Here, we deposit high N-doped carbon layers derived from melamine-formaldehyde resin in carbon nanotube (CNT) sponge networks, which can not only form the core−shell structure but also knot the network skeletons by binding interconnected CNTs, thus strengthening the 3D structures. The CNT sponges with high N-doped carbon layers have significantly enhanced mechanical properties including high elasticity, compressive stress, and Young's modulus. Meanwhile, composite sponges as lithium-ion capacitor (LIC) anodes can achieve a high specific capacity of 303 mAh/g, high rate capability, and long cyclic performance. The corresponding LIC cells with amorphous carbon cathodes can deliver a high energy density of 153 Wh/kg at 582 W/kg and 49 Wh/kg even at a high power density of 29.1 kW/kg. We provide a method to enhance 3D network structures, which have applications in freestanding electrode materials for flexible energy storage systems and microelectromechanical systems.