Due to the ultralow amounts of C3H8 and C2H6 gases, to design and synthesize water-stable MOFs that are promising for real-world efficient pipeline natural gas (NG) upgrading by the recovery of individual C3H8 and C2H6 gases is still a great challenge. Here, a N/O/F heteroatom-rich and rooflike [Cu(II)4Cu(I)2(COO)4(tetrazolyl)6] cluster-based ultra-microporous tsi-MOF (SNNU-Bai68) was afforded as a multiple heteroatom-rich and curved-surface-shaped cluster-based ultra-microporous MOF and the first porous MOF based upon such rooflike [Cu(II)xCu(I)y(tetrazolyl)z](2x+y-z)+ cluster. In SNNU-Bai68, the rooflike cluster was further assembled into a 1D chain secondary building block (SBB), which led to a high density of accessible potential adsorptive sites. Very interestingly, it exhibited the most promising balance of high gas adsorption uptakes at 0.01, 0.03, and 0.05 bar, high C3H8/CH4, C3H8/C2H6, and C2H6/CH4 adsorption selectivities, moderate adsorption enthalpies, and high water and chemical stability for pipeline natural gas upgrading by the recovery of individual C3H8 and C2H6 gases, which was further confirmed by the breakthrough experiments of the gas mixtures with/without 74% RH. Furthermore, the SC-XRD and GCMC studies revealed that the successful separation of C3H8, C2H6, and CH4 gases in SNNU-Bai68 is due to different synergistic effects of H-bonds between the frameworks at three adsorptive sites around each rooflike cluster and those different gas molecules, which were initially described systematically by the number of H atoms from the gas molecules, the total number of H-bonds within the synergistic H-bonds, and the binding energy of the framework at an adsorption site toward the gas molecules. In addition, this work may provide a method for the construction of a multiple heteroatom-rich and curved-surface-shaped cluster-based ultra-microporous MOF as a novel approach to build MOFs with polar pore surfaces, suitable pore sizes, and unique pore shapes to maximize the synergistic H-bonds between the framework and guests.