Evaluating the effect of ligand substitution on metal ions and/or clusters during the MOF growth process is conducive to rational design of isoreticular MOFs with improved performance. Through topological direction and ligand substitution strategy, we herein constructed two Sc-soc-MOFs (Sc-EBTC and Sc-ABTC) based on two similar rectangular-planar diisophthalate ligands, linear-shaped H4EBTC (1,1'-ethynebenzene-3,3',5,5'-tetracarboxylic acid) and zigzag-shaped H(4)ABTC (3,3',5,5'-azobenzenetetracarboxylic acid), under solvothermal conditions with formic acid as a modulator. {Sc[(Sc3O)-(H2O)(3)](3)(EBTC)(6)} (Sc-EBTC) possesses two distinct clusters as SBUs, trinuclear [Sc3O(CO2)(6)] (SBU1) and mononuclear cluster [ScO6] (SBU2), which maintain the soc-topology except for the mononuclear [ScO6] instead of the corresponding trinuclear [Sc3O(CO2)(6)] in Sc-ABTC ({(Sc3O)(H2O)(3)(ABTC)(1.5)(NO3)}). Notably, Sc-EBTC represents a rare soc-MOF with two distinct clusters as SBUs. Due to similar pore spaces, the two Sc-soc-MOF materials both exhibit enhanced and comparable gas sorption and selectivity performances. Specially, their remarkable C2H2, C2H4, and CO2 storage capacity along with prominent CO2/CH4 and C-2-hydrocarbons/CH4 separations indicate that these Sc-soc-MOFs are promising adsorbents for natural gas purification under ambient conditions.