The combination of biotechnology and artificial nanotechnology provide new breakthroughs in the design and manufacture of energy materials. In this work, the porous hollow hyphae carbon membrane with different thicknesses were acquired by biological cultivation approach, along with adsorbed Ni2+ as the in-situ growth points. Then, ultrafine hollow carbon tubes generated on the hyphae surface, forming multi-stage composite membrane (CNTs@MC) with tubules covering large tubes. Subsequently, rich amino functional groups were grafted onto MC (hyphae carbon membrane) surface to further improve its hydrophilicity and capacitance. In addition to the hollow structure, the hyphae carbon surface presents many small holes around 50 nm, which not only provides space for Ni2+ adsorption, but also favors the generation of double-layer capacitance. As secondary structure, ultrafine carbon nanotubes as microcircuits capture more charged ions on hyphae surface, thus offering better capacitance performance. The multistage hollow structure enhances the stability of material during ion adsorption. The grafted amino functional groups and intrinsic heteroatomic defects synergically enhance the wettability and pseudocapacitance of material. In general, large effective specific surface area, abundant surface amino functional groups and intrinsic heteroatomic defects guarantee the high capacitance of material, and also exhibits desirable performance in both solid-state supercapacitors and capacitive deionization applications. [Display omitted] • Microorganism construct 3D composite membrane autonomously. • A two-stage microcircuit built by in situ growth enhances the capacitance. • Interfacial modification improves the hydrophilicity and pseudocapacitance. [ABSTRACT FROM AUTHOR]