Three-dimensional (3D) all-carbon nanofibrous aerogels with good structural stability and elasticity are highly desirable in flexible energy storage/conversion devices. Hence, an efficient surface-induced co-assembly strategy is reported for the novel design and reconstruction of electrospun nanofibers into graphene/carbon nanofiber (CNF) composite aerogels (GCA) with hierarchical structures utilizing graphene flakes as cross-linkers. The as-obtained GCA monoliths possess interconnected macropores and integrated conductive networks, which exhibit high elasticity and great structural robustness. Benefitting from the largely increased surface area and charge-transfer efficiency derived from the multi-form firm interconnections (including pillaring, bridging and jointing) between graphene flakes and CNF ribs, GCA not only reveals prominent capacitive performance as supercapacitor electrode, but also shows excellent hydrogen evolution reaction activity in both acidic and alkaline solutions as a 3D template for decoration of few-layered MoSe2 nanosheets, holding great potentials for energy-related applications.