Separating helium (He) and hydrogen (H2), two gases that are extremely similar in molecular size and condensation properties, presents a formidable challenge in the helium industry. The development of membranes capable of precisely differentiating between these gases is crucial for achieving large‐scale, energy‐efficient He/H2 separation. However, the limited selectivity of current membranes has hindered their practical application. In this study, we propose a novel approach to overcome this challenge by engineering submicroporous membranes through the fluorination of partially carbonized hollow fibers. We demonstrate that the fluorine substitution on the inner rim of the micropore walls within the carbon hollow fibers enables tunability of the microporous architecture. Furthermore, it enhances interactions between H2 molecules and the micropore walls through the polarization and hydrogen bonding induced by C‐F bonds, resulting in simultaneous improvements in both He/H2 diffusivity and solubility selectivities. The fluorinated HFM‐550‐F‐1min membrane exhibits exceptional mixed‐gas separation performance, with a binary mixed‐gas He/H2 selectivity of 10.5 and a ternary mixed‐gas He/(H2+CO2) selectivity of 20.8, at 40 bar feed pressure and 35 oC, surpassing all previously reported polymer‐based gas separation membranes, and remarkable plasticization resistance and long‐term continuous stability over 30 days.