Carbon is one of the most important materials extensively used in industry and our daily life. Crystalline carbon materials such as carbon nanotubes and graphene possess ultrahigh strength and toughness. In contrast, amorphous carbon is known to be very brittle and can sustain little compressive deformation. Inspired by biological shells and honeycomb-like cellular structures in nature, we introduce a class of hybrid structural designs and demonstrate that amorphous porous carbon nanospheres with a thin outer shell can simultaneously achieve high strength and sustain large deformation. The amorphous carbon nanospheres were synthesized via a low-cost, scalable and structure-controllable ultrasonic spray pyrolysis approach using energetic carbon precursors. In situ compression experiments on individual nanospheres show that the amorphous carbon nanospheres with an optimized structure can sustain beyond 50% compressive strain. Both experiments and finite element analyses reveal that the buckling deformation of the outer spherical shell dominates the improvement of strength while the collapse of inner nanoscale pores driven by twisting, rotation, buckling and bending of pore walls contributes to the large deformation.