Abstract Given the scarcity of helium (He) resources, the application of scalable and energy‐efficient membrane‐mediated separation techniques for helium extraction holds substantial potential; however, few membrane materials have been reported for lean‐helium extraction from natural gas feeds (<1000 ppm). Herein, we present a facile strategy for fabricating the carbon molecular sieve (CMS) hollow fiber membranes with a hierarchical porous structure by tailoring the phase inversion behaviors of blend polymeric precursors and engineering the pyrolysis protocol. The CMS membranes composed of highly homogenized and inconsecutive macropores and size‐constrained ultramicropores in synergy exhibited superior separation performance in the separation of He/CH 4 . For instance, CA‐3‐700 membranes showed a He/CH 4 ideal selectivity of 1427 and He permeability of 521 barrer. In addition, the membrane presented superior mixed gas separation performances under simulated helium‐contained high‐pressure natural gas at hundred ppm levels (400–1300 ppm), while demonstrating long‐term continuous stability (from a quinary mixture of He/CH 4 /N 2 /C 2 H 6 /CO 2 ) over 120 h.