Abstract Adsorptive separation of propylene/propane (C 3 H 6 /C 3 H 8 ) mixture is desired for its potential energy saving on replacing currently deployed and energy‐intensive cryogenic distillation. Realizing efficient C 3 H 6 /C 3 H 8 separation in the emerging hydrogen‐bonded organic frameworks (HOFs) is very challenging owing to the lack of functional sites for preferential gas binding. By virtue of crystal engineering, we herein report a functionalized HOF ( HOF‐16 ) with free ‐COOH sites for the efficient separation of C 3 H 6 /C 3 H 8 mixtures. Under ambient conditions, HOF‐16 shows a significant C 3 H 6 /C 3 H 8 uptake difference (by 76 %) and selectivity (5.4) in contrast to other carboxylic acid‐based HOFs. Modeling studies indicate that free ‐COOH groups together with the suitable pore confinement facilitate the recognition and high‐density packing of gas molecules. The separation performance of HOF‐16 was validated by breakthrough experiments. HOF‐16 is stable towards strong acidity and water.