Etching single-layer graphene to incorporate a high pore density with sub-angstrom precision in molecular differentiation is critical to realize the promising high-flux separation of similar-sized gas molecules, e.g., CO2 from N2. However, rapid etching kinetics needed to achieve the high pore density is challenging to control for such precision. Here, we report a millisecond carbon gasification chemistry incorporating high density (>1012 cm−2) of functional oxygen clusters that then evolve in CO2-sieving vacancy defects under controlled and predictable gasification conditions. A statistical distribution of nanopore lattice isomers is observed, in good agreement with the theoretical solution to the isomer cataloging problem. The gasification technique is scalable, and a centimeter-scale membrane is demonstrated. Last, molecular cutoff could be adjusted by 0.1 Å by in situ expansion of the vacancy defects in an O2 atmosphere. Large CO2 and O2 permeances (>10,000 and 1000 GPU, respectively) are demonstrated accompanying attractive CO2/N2 and O2/N2 selectivities.