Purifying methane from natural gas using adsorbents not only requires the adsorbents to possess excellent separation performance but also to overcome additional daunting challenges such as humidity interference and durability requirements for sustainable use. Herein, porous organic crystals of a new macrocycle (CaC9) with superhydrophobic and self-healing features are prepared and employed for the purification of methane (>99.99% purity) from ternary methane/ethane/propane mixtures under 97% relative humidity. The high selectivity for methane and water-resistance are attributed to the unique chemical structure of CaC9, possessing an intrinsic 4.2 Å pore along with a pore environment modified with saturated alkyl chains. Besides, CaC9 crystals exhibit a self-healing capacity to realize in situ reconstruction of porosity within 15 min. The transformation of CaC9 crystals from a nonporous state to a porous state can be easily achieved upon treatment with n-hexane vapor, thereby presenting a novel solution to enhance the sustainable separation processes of porous materials. This work introduces a novel molecular-level porous adsorbent for natural gas separation, providing a valuable impetus for designing novel adsorbents with unexpected functions.