<p>The tuning of ligand linkage modes in porous crystalline materials to create isomers with varied properties is very meaningful, yet this approach remains rare in structural design and related photocatalytic applications. Here, we gain insight into the nature of this phenomenon based on isomerized metal-covalent organic frameworks (MCOFs) (i.e., MCOF-E and MCOF-Z) and discover that the specific selection of construction struts can result in E/Z ligand linkage mode with totally different stacking structures stimulated by temperature. Thus-obtained isomeric MCOFs exhibit different light absorption, charge transfer, and photocatalytic ability. Notably, the aniline generation efficiency in the nitrobenzene hydrogenation reaction of MCOF-E can reach up to 4.90 mM h⁻¹ with high conversion (∼100%) and selectivity (&gt; 99%), which is higher than MCOF-Z and other contrast counterparts. Theoretical calculations reveal that MCOF-E possesses a narrower band gap than MCOF-Z, which facilitates the more efficient generation of photo-induced carriers. This enhanced carrier generation thereby accelerates the reaction kinetics, which in turn leads to a significant improvement in nitrobenzene hydrogenation efficiency.</p>