Abstract Bacteria‐derived carbon anode materials have shown appealing potential for advanced energy storage applications due to their low cost and good sustainability. However, the few intrinsic defects, sluggish transmission dynamics, and low capacity become the main bottleneck for their further development. Herein, the study designs a highly B, N co‐doped mesoporous carbon (BNMC)/staphylococcus aureus‐derived carbon (SAC) composite via a facile assembly route, followed by boron‐doping. Enabled by heteroatom doping and pore construction, the resulting BNMC/SAC anode for lithium‐ion batteries demonstrates a high reversible capacity of 621.77 mAh g −1 at 200 mA g −1 even after 500 cycles, and an excellent rate performance of 405.14 mAh g −1 at 2 A g −1 . Importantly, in situ/ex situ characterizations and theoretical simulation results further unveil that high B, N co‐doping along with a small amount of P doping can significantly increase the intrinsic defects of BNMC/SAC, thus providing more active sites for lithium‐ion storage. Furthermore, these structural features are conducive to improving the interfacial stability of the whole electrode, achieving a thin and uniform SEI film. The multi‐component co‐doping strategy along with pore engineering presents a scalable approach for enhancing the interfacial stability and transfer dynamics of carbon‐based electrode materials for low‐cost energy storage.