Polymorphism in metal−organic frameworks (MOFs) means that the same chemical building blocks (nodes and linkers) can be used to construct isomeric MOFs with different topological networks. The choice of topology can substantially impact the pore network of the MOF, changing the sizes and shapes of the pores, which has implications for adsorption and separation applications. In this work, we look at the influence of topology in 38 polymorphic MOFs on the separation of linear and branched C4–C6 alkane isomers, a separation of great importance to the petrochemical industry. We find that the MOF Cu2(1,4-benzenedicarboxylate) in nbo topology (nbo-Cu2BDC) has particularly high affinity for linear alkanes due to its small pore size, which excludes the branched isomers. Upon studying this MOF in further detail, we find that it can take either of two conformations: a cubic conformation, which is typical of nbo MOFs, and a unique star conformation that contains 1D triangular and hexagonal channels. The determination of which conformation the MOF will adopt depends on steric effects between the nodes and linkers.