Aqueous zinc‐ion batteries (AZIBs) are promising candidates for large‐scale energy storage due to the high safety and cost effectiveness. Yet it is suffered from the obscurely uncontrolled Zn2+ deposition that accumulates together and easily penetrates the separator. Here, a 3D long‐range ordered polyacrylonitrile (PAN) nanofiber separator is designed to overcome this barrier. The N atoms on the surface of separator uniformly distribute the ion flux and guide the cation transport through available N–Zn bonds. Hence, the electric field on the anode is evenly distributed, which helps to guide the nucleation, growth, and deposition of zinc ions. Benefit from this functional group, a Zn symmetric cell with PAN separator shows a long‐term stability and dendrite‐free deposition layer with a preferred (101) crystallographic orientation. Meanwhile, the Zn/NH4V4O10 cells display high specific capacity and excellent long‐term durability of 89.2% capacity retention after 1500 cycles at 10 A g−1. This work demonstrates the design of functional separator provides an effective way to modify Zn2+ deposition behavior and achieve a dendrite‐free Zn metal anode.