Enriching the structural diversity of metal–organic frameworks (MOFs) is of great importance in developing functional porous materials with specific properties. New MOF structures can be accessed through the rational design of organic linkers with diverse geometric conformations, and their structural complexity can be enhanced by choosing linkers with reduced symmetry. Herein, a series of Zr‐based MOFs with unprecedented topologies were developed through a linker desymmetrization and conformation engineering approach. A tritopic carboxylate linker with reduced symmetry and flexible triangular geometry was designed to construct three Zr‐based MOFs (denoted as NU‐57, NU‐58, and NU‐59) by modulating synthetic conditions. Notably, the conformational flexibility and reduced symmetry of the linker generated two unprecedented topologies in NU‐58 and NU‐59. Furthermore, solvent removal in NU‐58 via thermal activation process produced missing linker defects. Finally, the adsorption behavior of these MOFs towards alkanes and alkenes was studied to gain insights into their structure‐property relationships, which demonstrated that NU‐57 and NU‐58 exhibit unusual reverse selectivity for alkanes in alkane/alkene separations. Overall, this work highlights the rational design of linkers using a desymmetrization strategy as a powerful method to enrich the structural diversity of MOFs and to access novel MOFs with unique properties.