Creating molecular networks with different topologies using identical molecular linkers is fundamentally important but requires precise chemistry control. Here, we propose an effective strategy to regulate the network topologies of two-dimensional (2D) covalent organic frameworks (COFs) through the conformational switching of molecular linkages. By simply altering the substituents of an identical molecular linker, the topology-selective synthesis of two highly crystalline 2D COFs can be readily achieved. Their distinct crystal structures are observed and determined by low-dose, high-resolution transmission electron microscopy imaging, indicating that the driving force for linkage conformation switching is intramolecular hydrogen bonding. Our strategy would greatly diversify the COF topologies and enable vast postsynthetic modifications such as boron complexation, endowing these structures with a unique optical property such as fluorescence turn on and aggregation-induced emission.