Two-dimensional covalent organic frameworks (2D COFs) are well-defined polymeric sheets that usually stack in an eclipsed mode via van der Waals forces. Extensive efforts have been made to manipulate interlayer interactions, yet there still lack a way to construct conjugated connections between adjacent layers, which is important for (opto)electronic-related applications. Herein, we report an interlayer topological polymerization strategy to transform the well-organized diacetylene columnar arrays in three different 2D COFs (TAPFY-COF, TAPB-COF, and TAPP-COF) into conjugated enyne chains upon heating in the solid state. The resultant COFs (COF-P) with retained high crystallinity possess broadened absorption bands and narrowed band gaps. The newly formed conjugated chains provide extra charge carrier pathways through direct π-electron delocalization. As a proof-of-concept, after topological polymerization, the conductivity of the TAPFY-COF film achieves 2.8 × 10-4 S/cm without doping, and the photothermal, photoacoustic, and oxygen reduction catalytic performance of TAPP-COF is significantly improved.