The combination of structural rigidity and optimal pore dimensions of the resulting Zr-MOFs has placed them as ideal sorbents for the separation of industrially significant alkane mixtures. They showed that HIAM-802 and HIAM-601 with high stability and distinct pore apertures, can efficiently discriminate hexane isomers as a function of branching through selectively molecular exclusion mechanism. The molecular sieving mechanism was elucidated by density functional theory simulations and the practical separation performances were validated by extensive breakthrough experiments. In conclusion, this work not only develops a general synthetic protocol for creating uniform ultramicroporosity in Zr-MOF crystals, but also establishes a unique linker design principle for achieving controllable assembly of reticular sorbents for advanced separations.