Developing energy-efficient alternatives for pressure swing adsorption for methane separation from unconventional natural gas is crucial and challenging in the petrochemical industry. Herein, a heptazine-based porous MOF featuring a triple-layered supramolecular framework built on 2D stacked honeycomb layers was reported, which revealed 1D elliptic channels decorated with high concentrations of binding sites arising from unsaturated metal sites and exposed N atoms. The MOF displays high C2 and CO2 loadings and IAST selectivities with respect to CH4. The molecular simulation reveals that a high concentration of binding sites in 1D elliptic channels accounts for the highly selective separation of methane.