 Nanofibrillated cellulose with the features of nano-scale fibers and self-assembly has attracted significant attention to acquire porous structure for low-cost and high-performance electrode materials. Here, a carbon nanofiber aerogel was prepared by self-assembling the building-blocks of nanofibrillated cellulose into controlled macro and mesoporous structure. A typical activation was further applied to engineer abundant micropores, which led to narrowed carbon walls as well as improved surface area (1726 m2 g−1). Due to the facile-constructed hierarchical pore structure and large ion-accessible surface area, the resultant carbon aerogel exhibited comparable performance to reported electrodes from porous bio-carbons. It displayed a high specific capacitance of 169 F g−1 at a high current of 20 A g−1, retaining 73% of that at 0.2 A g−1 (231 F g−1). Furthermore, the symmetric supercapacitor showed a high capacitance retention during the long-term charge–discharge. This work provides a facile and renewable way to develop hierarchical porous bio-carbons with high charge storage capability.