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Single‐layer crystalline films are ideal separation membrane materials because their atomic thickness could yield the highest possible molecular flux once nanopores are generated. However, the development of single‐layer membranes with well‐defined pore structures remains elusive, which makes the realization of efficient molecular sieving and interpretation of molecular transport a difficult task. Herein, we report the fabrication of single‐layer nanoporous hexagonal boron nitride (hBN) membranes that uniquely contain triangular nanopores with a high density (around 1012 pores per cm2). The hBN membranes exhibit a H2 permeance of 5.43 × 10−6 mol m−2 s−1 Pa−1 with a H2/CH4 selectivity of 14.7; they also show a CO2 permeance of 1.37 × 10−6 mol m−2 s−1 Pa−1, with a CO2/N2 selectivity of 12.3. Importantly, we show that straightforward mathematical modeling can predict and describe the gas transport properties of the hBN, providing new insights into the molecular transport across atomically thin nanopores. The results gained from this study could significantly advance our understanding of molecular transport across hBN nanopores and may promote the development of hBN membranes to address critical separation issues.