Two isostructural metal organic frameworks (MOFs) having micropores of the same "static aperture size" but different "effective aperture size" have been prepared using 5-(pyridin-3-ylethynl)isophthalic acid as a ligand having two different types of functional units, an isophthalate (iph) unit and a pyridyl unit, simultaneously in a single ligand. The combination of iph unit and Cu (or Zn) ion led to two-dimensional layers of Kagome (kgm) net topology, the layers being further pillared by the internal auxiliary pyridyl unit to form a three-dimensional microporous framework having two different types of cage-like pores, cage A and cage B, with different aperture sizes and shapes. (1) The MOFs can distinguish the adsorbates (N-2/Ar) not based on the widely used kinetic diameters of the adsorbates but based on the minimum diameters of the adsorbates, which are more shape dependent. While cage A with a sufficiently large aperture size compared with the size of the adsorbates does not show any size selectivity, cage B with an approximate size match between the adsorbates and the pore apertures shows shape selectivity for the adsorbates. The smaller but spherically shaped Ar atom is not allowed into the pore with the oval-shaped aperture; however, the larger linear N-2 molecule is allowed into the pore with the oval-shaped aperture. (2) Even though the two isostructural MOFs have the same static aperture size of cage B, they show different size selectivity for the adsorbates based on the effective aperture size, which reflects the different extents of the framework flexibility.