Aqueous zinc ion batteries (AZIBs) have been regarded as one of the most promising energy storage systems because of their security, high specific capacity and abundant zinc resources, etc. Despite the promising prospects of AZIBs, their practical application is still plagued by dendrite and side reactions on zinc surface. In this paper, glass fiber separators were modified by in-situ loading metal-organic framework MIL-125 (M-125) and its -NH2-functionalized material (NM-125). The designed separator pore structure was successfully adjusted and endowed with -NH2 functional groups, which can ultimately dramatically enhance the electrochemical performance of AZIBs under practical operation conditions. The functionalized NM-125 with smaller pore size and particle size enables NM-125-GF to prevent the transport of macromolecular anions in the electrolyte, guiding and promoting zinc ions to undergo an orderly migration. In addition, -NH2 of NM-125 can adsorb Zn2+ and detach them from the solvated structure, inhibiting the generation of anode-side reactions and optimizing battery performance. Notably, Zn||MnO2 full cell assembled with -NH2 functionalized separator also shows a high initial discharge specific capacity (160.2 mAh g-1) with a high capacity retention of ∼99.8% even after 700 cycles. The rational design of the functionalized separator provides a useful guideline for optimizing high-performance AZIBs.