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• A facile method was reported by us to sustainably obtain 3D and defective nanocarbon from waste RS residue. • The key role of bacterial played in the formation of RS residue with unque structure and composition was revealed. • The underlying pyrolysis mechanism of RS residue is explored. • The obtained bio-char was demonstrated as a promising candidate for supercapacitor. Defective carbon nanomaterials with three-dimensional (3D) structure are showing great potential for advanced electrochemical storage and conversion devices, but its application is restricted by the synthesis, which is usually involved with complicate and energy-intensive processes. Herein, pyrolysis of rice straw (RS) residue, of which is collected from the bacterial assisted hydrolysis, is proposed by us here, and the obtained bio-char is defective with 3D structure and rich in oxygen-containing functional groups. Compared to the pristine one, specific surface area of the representative RS carbon (RSC2) was increased from 428.8 to 1131.7 m2 g−1. The assembled supercapacitor with RSC2 showed a high specific capacitance of 331F g−1 at a charge–discharge current density of 0.5 A g−1, and a capacity retention of 97.6% was maintained at 5 A g−1 even after 10,000 cycles. [ABSTRACT FROM AUTHOR]