The development of three-dimensional carbon-based nanostructures is the next step forward for boosting industrial applications of carbon nanomaterials such as graphenes and carbon nanotubes. Some defects, which have been considered as detrimental factors for maintaining exceptional materials properties of two-dimensional graphene, can be actively used to synthesize three-dimensional graphene-based carbon nanostructures. Here we describe a fast and heretofore unreported defect-engineered method to synthesize three-dimensional carbon nanohybrid structures with strong bonding between graphene nanoplatelets and carbon nanotubes using simple microwave irradiation and an ionic liquid. Our one-pot method utilizes defect-engineered sequential processes: microwave-based defect generation on graphene nanoplatelets, anchoring of palladium nanoparticles on these defects, and subsequent growth of carbon nanotubes by use of an ionic liquid. The unique three-dimensional nanostructures showed an ultrahigh redox capacitance due to high porosity, a high surface-to-volume ratio from the spacer role of vertically standing one-dimensional carbon nanotubes on graphene sheets, and capacitance-like redox response of the palladium nanoparticles. The proposed defect-engineered method could lead to novel routes to synthesizing three-dimensional graphene-based nanostructures with exceptionally high performance in energy storage systems.