The development of highly efficient separation technology for the purification of natural gas by removing ethane (C2H6) and propane (C3H8) is a crucial but challenging task to their efficient utilization in the chemical industry and social life. Here, we report three isomorphic ultra-microporous metal-organic frameworks (MOFs), M-pyz (M = Fe, Co, and Ni, and pyz = pyrazine) referred to as Fe-pyz, Co-pyz, and Ni-pyz, respectively, which possess high density of open metal sites and suitable pore structure. Compared with the benchmark materials reported, M-pyz not only has high adsorption capacities of C2H6 and C3H8 at low pressure (up to 51.6 and 63.7 cm3·cm−3), but also exhibits excellent C3H8/CH4 and C2H6/CH4 ideal adsorption solution theory (IAST) selectivities, 111 and 25, respectively. Theoretical calculations demonstrated that the materials’ separation performance was driven by multiple intermolecular interactions (hydrogen bonding interactions and van der Waals effect) between gas molecules (C2H6 and C3H8) and the M-pyz binding sites. And, dynamic breakthrough experiments verified the superior reusability and practical separation feasibility for the ternary CH4/C2H6/C3H8 mixtures. Furthermore, M-pyz can be synthesized rapidly and on a large scale at room temperature. This work presents a series of promising MOFs adsorbents to efficiently purify natural gas and promotes the industrial development process of MOFs materials.