Etching an ensemble of vacancy defects (nanopores) in single-layer graphene (SLG) to obtain a high density of nanopores with an effective size that enables high-performance gas sieving is challenging. This is because nanopore nucleation and expansion are usually coupled. Aggressive etching conditions that promote defect nucleation are difficult to control for limiting the pore expansion. To address this, we recently reported a millisecond gasification reactor (MGR) that allows aggressive etching and at the same time restricts the pore expansion time to a few milliseconds. Herein, we systematically analyze various components of the MGR setup and achieve optimal conditions based on a mathematical model simulating the etchant exposure profile in MGR. We study the effect of the etching conditions such as baseline pressure, peak pressure, and exposure time, on the defect formation in SLG via Raman spectroscopy. Nanopores formed at different etching temperatures are observed by scanning tunneling microscope, revealing the relationship between the etching temperature and the pore density. The incorporation of nanopores in SLG under the optimized conditions allows the realization of extremely attractive CO2-sieving performances from the nanoporous SLG (NSLG) membranes, marked by CO2 permeance of 900–4000 gas permeation units (GPU) and CO2/N2 selectivity of 17–25. This study establishes MGR as a highly tunable etching tool for incorporating the desired ensemble of nanopores in graphene for a number of important molecular separations.