Annular tetranuclear cluster based metal–organic frameworks (MOFs) have displayed unique advantages in gas adsorption and separation due to their highly connected robust architectures. Herein, two novel heterometallic tetranuclear motifs, [Y2Cd2(μ3-O)2(COO)8(H2O)2] and [Y2In2(μ3-O)2(μ2-O)2(COO)8(H2O)2], were successfully explored, which were further extended by 1,3,5-tris(4-carboxyphenyl)benzene (H3BTB) tritopic linker to give isostructural MOFs (SNNU-326 and -327). SNNU-326 and -327 both exhibit the abilities to remove impurities (C2-hydrocarbons and CO2) in natural gas (NG) and excellent CH4 storage capacities at high pressures. SNNU-326 shows better CH4 purification and storage performance than SNNU-327 owing to different framework charges, in which only one counter ion is needed in SNNU-326 but two of them are necessary for SNNU-327, thus resulting in an obvious decrease of surface area. Dynamic breakthrough experiments demonstrate that SNNU-326 can effectively separate CH4 from equimolar C2H2/CH4, C2H4/CH4, C2H6/CH4, and CO2/CH4 mixtures with breakthrough interval times of about 40.6, 35.1, 54.2, and 10.2 min g–1 (273 K, 1 bar, 2 mL min–1), respectively. At the same time, SNNU-326 exhibits excellent CH4 storage capability with total and working uptakes of 154.3 cm3 (STP) cm–3 (80 bar) and 103.4 cm3 (STP) cm–3 (5–65 bar) at 273 K on account of the collaborative impacts of adequate apertures, high surface areas, and multiple open metal sites.