The discovery of appropriate synthetic reaction conditions for fabricating a stable zirconium-based molecular sieve (Zr-fum-fcu-MOF) with minimal defects and its utilization in the challenging separation of linear paraffins from branched paraffins is reported. The crystallinity and structural defects were modulated and adjusted at the molecular level by controlling the synthetic reaction conditions (i.e., amounts of modulators and ligands). The impact of molecular defects on the separation of n-butane from iso-butane was studied through the preparation, fine characterization, and performance evaluation of Zr-fum-fcu-MOFs with varying degrees of defects. Defect-rich Zr-fum-fcu-MOFs were found to have poor n-butane/iso-butane separation, mainly driven by thermodynamics, while Zr-fum-fcu-MOFs with fewer or minimal defects showed efficient separation, driven mainly by kinetics and full molecular exclusion mechanisms. The impact of intrinsic defects (i.e., missing organic or inorganic blocks) on the associated mechanisms involved in the separation of n-butane/iso-butane was evidenced through single-gas adsorption, mixed-gas column breakthrough experiments, and calorimetric studies. This investigation demonstrates, for the first time, the importance of controlling intrinsic defects to maintain the selective exclusion behavior of hydrocarbon isomers when using molecular sieves.