Zeolite-like supramolecular assemblies (ZSAs) are a distinctive class of hydrogen-bonded organic frameworks (HOFs) that form zeolite-like structures using fundamental four-membered ring (4MR) building units, known as metal-organic squares (MOS). Herein, we developed a zeolite-like supramolecular assemblies (ZSAs) platform to precisely control hydrogen-bond directionality, coupled with confinement effects, ultimately synthesizing two isoreticular HOFs, ZSA-12 and ZSA-13, with distinct pore environments. Notably, owing to their microporous structures, ZSA-12 and ZSA-13 exhibited exceptional CO2 adsorption capacity and ultra-high CO2/CH4 separation selectivity. The IAST selectivity value of 98.4 sets a benchmark, surpassing all previously reported HOFs. Theoretical calculations and breakthrough experiments confirmed the outstanding separation capability of ZSA-12 and ZSA-13, both of which also demonstrated remarkable thermal and chemical stability. Furthermore, gram-scale synthesis of ZSA-12 and ZSA-13 was successfully achieved under mild conditions using pure water as the solvent—one of the few reported HOFs that can be synthesized in large quantities via a water-based process at an exceptionally low cost. Thus, ZSA-12 and ZSA-13 offer a new strategy for the synthesis of isoreticular HOFs and hold great promise for biogas purification and upgrading applications.