Uncontrollable dendrite growth and sluggish ion‐transport kinetics are considered as the main obstacles for the further development of high‐performance aqueous zinc ion batteries (AZIBs). Here, a nature‐inspired separator (ZnHAP/BC) is developed to tackle these issues via the hybridization of the biomass‐derived bacterial cellulose (BC) network and nano‐hydroxyapatite particles (HAP). The as‐prepared ZnHAP/BC separator not only regulates the desolvation process of the hydrated Zn2+ ions (Zn(H2O)62+) by suppressing the water reactivity through the surface functional groups, alleviating the water‐induced side‐reactions, but also boosts the ion‐transport kinetics and homogenize the Zn2+ flux, resulting in a fast and uniform Zn deposition. Remarkably, the Zn|Zn symmetric cell with ZnHAP/BC separator harvests a long‐term stability over 1600 h at 1 mA cm−2, 1 mAh cm−2 and endures stable cycling over 1025 and 611 h even at a high depth of discharge (DOD) of 50% and 80%, respectively. The Zn|V2O5 full cell with a low negative/positive (N/P) capacity ratio of 2.7 achieves a superior capacity retention of 82% after 2500 cycles at 10 A g−1. Furthermore, the Zn/HAP separator can be totally degraded within 2 weeks. This work develops a novel nature‐derived separator and provides insights in constructing functional separators toward sustainable and advanced AZIBs.