Aqueous zinc-ion batteries (AZIBs) are increasingly being acknowledged as a promising candidate to safely power large-scale energy storage systems and portable devices. However, the development of effective separator materials remains a significant challenge due to issues such as harmful dendrite growth on zinc (Zn) anodes and parasitic side reactions in aqueous electrolytes. To address this challenge, we synthesize a manganese-coordinated cellulose nanofibril (Mn-CNF)-based separator for high-performance AZIBs. This separator affords enhanced ion transport channel, a large number of hydroxyl groups, and exceptional mechanical properties, with a tensile strength of 2.8 MPa and superior ionic conductivity of 5.14 mS·cm−1. These attributes collectively enhance Zn-ion transport, minimize nucleation overpotential for Zn, and accelerate the Zn deposition kinetics, thus significantly outperforming the untreated CNF separators. Consequently, the Zn||MnO2 battery with the Mn-CNF separator shows a marked improvement in the galvanostatic rate performance and cycling stability by effectively accelerating and optimizing Zn-ion transport. This study offers valuable insights into the development of efficient and reliable separators for advanced electrochemical energy storage technologies.