A series of mixed-linker metal-organic frameworks [Zn₂(Xiso)₂(pcih)₂]_n containing substituted isophthalate linkers (Xiso^2- X = OH or CH₃ or NH₂ or H) and 4-pyridinecarbaldehyde isonicotinoyl hydrazone pillars (pcih) have been prepared by using both solution and mechanochemical methods. Single-crystal X-ray diffraction reveals their interdigitated two-dimensional structures with different arrangements of layers, dependent on hydrogen bonding and CH···π interactions involving the substituents and/or linkers. These supramolecular interactions are responsible for the formation of interlayer pores of various volumes, shapes, and dimensionality. All materials exhibit selective gas adsorption of CO₂ over N₂ with diverse profiles. Polar groups (OH and NH₂) of the isophthalate linkers increase chemical affinity to carbon dioxide as well as hydrolytic and thermal stability of the frameworks.