Supercapacitor electrodes (SCs) of carbon-based materials with flexible structures and morphologies have demonstrated excellent electrical conductivity and chemical stability. Herein, a clean and cost-effective method for producing a 3D self-doped honeycomb-like carbonaceous material with KOH activation from bio-waste oyster shells (BWOSs) is described. A remarkable performance was achieved by the excellent hierarchical structured carbon (HSC-750), which has a large surface area and a reasonably high packing density. The enhanced BWOSs-derived HSC-750 shows an ultrahigh specific capacitance of 525 F/g at 0.5 A g−1 in 3 M KOH electrolyte, as well as high specific surface area (2377 m2 g−1), pore volume (1.35 cm3 g−1), nitrogen (4.70%), and oxygen (10.58%) doping contents. The SCs also exhibit exceptional cyclic stability, maintaining 98.5% of their capacitance after 10,000 charge/discharge cycles. The two-electrode approach provides a super high energy density of 28 Wh kg−1 at a power density of 250 W kg−1 in an alkaline solution, with remarkable cyclability after 10,000 cycles. The study demonstrates the innovative HSC synthesis from BWOSs precursor and cost-effective fabrication of 3D N/O self-doped heteroatom HSC for flexible energy storage.