The rising demand for helium resources makes the effective separation of helium from natural gas increasingly important in the cryogenics industry and welding technology. However, most commonly used membranes cannot efficiently separate helium from the small molecules in natural gas. In this work, using first-principles calculations, combined with molecular dynamics simulations, we showed that efficient separation of helium from natural gas molecules (H2O, CO2, CO, CH4, and N2) as well as noble gas molecules (Ne and Ar) can be achieved in an inorganic graphenylene (IGP) membrane with high selectivities. In particular, molecular dynamics simulations demonstrated that high helium permeance (approximately 10−4 mol m−2 s−1 Pa−1) can be achieved over a wide range of temperatures (100 to 500 K) with high selectivity over other gas molecules. The high permeance and selectivity of the IGP monolayer membrane to helium are quite promising for industrial applications.