A novel nickel skeleton 3D nitrogen doped graphene (N-GR/NF) superstructure with interconnected graphene nanosheets and nanoscrolls was synthesized using a facile two-step method. By varying the precursor concentration, the assembly of a graphene aerogel can be easily regulated, yielding different micro-structures and morphologies which accelerate the fast electron/ion transportation. The N-GR/NF composites demonstrate enhanced capacitance of 250 F g-1 at 5 A g-1, good rate performance (237 F g-1 at the current density of 12 A g-1) and cycle stability (90.9% retention after 5000 cycles) in 1 M KOH electrolyte. This study provides a new strategy for the microporous engineering of graphene gel, promising for further exploitation in various other applications.