A separator is essential component for securing the safety and stability of secondary batteries. Sodium ion batteries (SIBs) have been considered as a highly powerful next generation energy storage device, but the conventionally used glass fibre (GF) separators for SIBs do not meet the necessary standards due to their randomly distributed pore structure, which causes severe safety problems and capacity decay. Although many studies have been performed to address these drawbacks, there are still difficulties of controlling the inner pore structure of GF. Herein, a strategy is introduced to control the inner porous nanostructure of GF via non-solvent induced phase separation (NIPS) engineering for the gel-polymer electrolyte in SIBs. We report how different types of porous polymer gel electrolyte inside the GF matrix affect SIB performance in terms of both pore nanostructure and vertical position of polymer layer. As a result of NIPS, the optimized gel-polymer electrolyte in GF facilitates increased ionic conductivity via modified ion transport and displays superior cell characteristics with excellent stability.