LiFePO4 (LFP) is recognized as a promising electrode material for capturing lithium ions (Li+); however, the presence of antisite defects in LFP crystals blocks the one-dimensional (1D) diffusion channel along the b-axis, thereby slowing down Li+ diffusion and compromising cycling stability. Herein, we propose a “microbial enzyme-catalyzed” green synthesis strategy, successfully preparing polymorphic LFPs characterized by a low concentration of antisite defects (< 3 %), resulting in enhanced ion transport and stable cycling performance. The low-concentration antisite defective LFP provided a smooth ion diffusion channel, enhancing both Li+ diffusion and electron transport to effectively improve kinetics. Additionally, the carbon shell derived from polyphosphorus bacteria improved electrical conductivity and provided space to accommodate the volume expansion of LFP, ultimately enhancing cycling stability. Consequently, LFP@C-7 exhibited excellent Li+ capture capacity (3.05 mmol g−1) and rate (1.01 mmol g−1min−1), with a high separation factor of 212 (Mg/Li ratio of 60) and excellent cycling stability (capacity retention exceeding 83.3 % over 100 cycles). Electrochemical quartz crystal microbalance (EQCM-D) analysis confirmed the three-stage reaction of hydration, ion exchange, and desorption during Li+ capture by LFP@C-7. Furthermore, in-situ X-ray diffraction (XRD) demonstrated a reversible phase transition mechanism (FePO4→LiFePO4→FePO4) throughout the Li+ insertion and extraction cycles. This study provides a new feasible solution for the green synthesis of low-concentration antisite defects LFP.