Carbon nanotubes/graphene hybrid materials with excellent physicochemical properties can be widely applied in the fields of energy storage, electrocatalysis, sensing, etc. Reducing the self-stacking and achieving covalent interaction between carbon nanotubes and graphene are important to ensure a stable hierarchical architecture and effective mass transfer. Herein, we propose a one-step strategy to synthesize 3D interconnected carbon nanotubes/graphene hybrids on the easy-to-remove biomass-derived substrate. The calcined natural cuttlebone as bi-functional catalyst precursor can simultaneously grow carbon nanotubes and graphene by one-step chemical vapor deposition without the addition of extra metal catalysts, while the interconnected structure can act as the porous template for graphene growth. The simultaneous growth process can obtain covalent bonding between carbon nanotubes and graphene, while the crystalline quality and interlayer space can be adjusted by different carbon sources and growth parameters (e.g., temperature). The one-step grown carbon nanotubes/graphene hybrids with seamless interfaces and hierarchical interconnected 3D structure can effectively enhance the electron transfer as well as the electrolyte infiltration efficiency. When utilized as lithium-ion batteries (LIBs) anode, a high specific capacity (544 mAh g–1 at 0.1 A g–1), good rate capability (200 mAh g–1 at 6.4 A g–1 with an ultrashort charge time of 113 s), and excellent cyclic stability can be achieved. This simple and one-step carbon nanotubes/graphene hybrids fabrication strategy can be easily scale-up and applied in various fields.