Based on the hard-soft acid base (HSAB) theory, three robust isoreticular metal-organic frameworks (MOFs) with nia topology were successfully synthesized by solvothermal reaction {[In3O(BHB)(H2O)3]NO3·3DMA (JLU-MOF110(In)), [Fe3O(BHB)(H2O)3]NO3 (JLU-MOF110(Fe)), and [Fe2NiO(BHB)(H2O)3] (JLU-MOF110(FeNi)) (DMA = N,N-dimethylacetamide, H6BHB = 4,4″-benzene-1,3,5-triyl-hexabenzoic acid)}. Both JLU-MOF110(In) and JLU-MOF110(Fe) are cationic frameworks, and their BET surface areas are 301 and 446 m2/g, respectively. By modification of the components of metal clusters, JLU-MOF110(FeNi) features a neutral framework, and the BET surface area is increased up to 808 m2/g. All three MOF materials exhibit high chemical and thermal stability. JLU-MOF110(In) remains stable for 24 h at pH values ranging from 1 to 11, while JLU-MOF110(Fe) and JLU-MOF110(FeNi) persist to be stable for 24 h at pH from 1 to 12. JLU-MOF110(In) exhibits thermal stability up to 350 °C, whereas JLU-MOF110(Fe) and JLU-MOF(FeNi) can be stable up to 300 °C. Thanks to the microporous cage-based structure and abundant open metal sites, JLU-MOF110(In), JLU-MOF110(Fe), and JLU-MOF110(FeNi) have excellent CO2 capture capacity (28.0, 51.5, and 99.6 cm3/g, respectively, under 298 K and 1 bar). Interestingly, the ideal adsorption solution theory results show that all three MOFs exhibit high separation selectivity toward CO2 over N2 (35.2, 43.2, and 43.2 for CO2/N2 = 0.15/0.85) and CO2 over CH4 (14.4, 11.5, and 10.1 for CO2/CH4 = 0.5/0.5) at 298 K and 1 bar. Thus, all three MOFs are potential candidates for CO2 capture and separation. Among them, JLU-MOF110(FeNi) displays the best separation potential, as revealed by dynamic column breakthrough experiments.