Tröger's base (TB) polymer of intrinsic microporosity has aroused increasing attention in various membrane-mediated gas separations. Herein we report macromolecular engineering to tune the microporosity of Tröger's base polymer of intrinsic microporosity (TB-PIM) via ionization for highly permselective helium recovery from natural gas. We reveal that the ionization of TB-PIM tightens polymer chain-packing, leading to dramatic enhancement of gas selectivities. Consequently, the ionic ITB-PIM membranes display the He/CH4 selectivity increments in the range of 34–158% and impressively high gas selectivities for helium recovery (i.e., α(He/CH4) = 246; α(He/N2) = 229). Due to the enhancement of inter-chain interactions induced by electrostatic interaction, the ITB-PIM membranes exhibit enhanced plasticization resistance compared to the pristine TB-PIM membranes. Notably, the ITB-Trip membrane showed excellent low-temperature gas separation performance with a He permeance of 3162 Barrer and He/CH4 selectivity of 38.5 at −30 °C, far beyond the 2008 upper bound. It is also proved that the microporosity and gas separation performance of ITB-PIM membranes is highly tailorable by adjusting the TB monomer structure. The facile functionalization method, highly diverse tunability, and excellent gas separation performance render the ITB-PIM membranes promising for helium recovery from natural gas.