The separator is an essential component of sodium-ion batteries (SIBs) to determine their electrochemical performances. However, the separator with high mechanical strength, good electrolyte wettability and excellent electrochemical performance remains an open challenge. Herein, a new separator consisting of amphoteric nanofibers with abundant functional groups was fabricated through supramolecular assembly of natural polymers for SIB. The uniform nanoporous structure, remarkable mechanical properties and abundant functional groups (e.g. −COOH, −NH₂ and −OH) endow the separator with lower dissolution activation energy and higher ion migration numbers. These metrics enable the separator to lower the barrier for desolvation of Na⁺, accelerate the migration of Na⁺, and generate more stable solid electrolyte interphase (SEI) and cathode electrolyte interphase (CEI). The battery assembled with the amphoteric nanofiber separator shows higher specific capacity and better stability than that assembled with glass fiber (GF) separator.