Biomass-derived hard carbons (HCs) present significant opportunities for low-cost and high-performance sodium-ion batteries, but face the dilemma of low specific capacity and inadequate cycling stability. The exploration of biomass-derived HCs with electron-rich heteroatoms and nanopores structure has the potential to enhance the electrochemical performance by providing more active sites, expanding graphite spacing, and facilitating sodium ions transport. However, designing biomass-derived HCs that incorporate both electron-rich heteroatoms and nanopores remains a challenge. Herein, we report the use of microorganism’s bioactivity and cell membranes as space-confined reactors to create N and P co-doped HCs with a nanopore structure. And the influence of microorganism bioactivity on the preparation of HCs is explored. As expected, the yeast cell-derived hard carbons in glucose solution (YHCs-G) exhibit an impressive initial coulombic efficiency (ICE) of 84.6?%, a remarkable reversible capacity of 320.3 mAh g?1 at 0.1?C, and favorable cycling stability, retaining 77.5?% capacity at 10?C even after 15,000 cycles, with only a 0.0015?% capacity decay per cycle. Furthermore, the sodium storage mechanism of “adsorption-intercalation-pore filling” is evidenced by charge-discharges curves, in-situ Raman spectroscopy, in-situ X-ray diffraction and galvanostatic intermittent titration technique. This study offers a new insight and strategy for preparing N and P co-doped biomass-derived hard carbons with nanopore structure, highlighting the potential use of microorganisms and their bioactivity for stable and fast-charging of HCs in sodium-ion batteries.