To better understand the structure–catalytic property relationship, a platform of urea-containing MOFs with diverse topologies as hydrogen-bonding (H-bond) catalyst has been well established in the present work. During the construction of MOFs, we proposed a new strategy called the isoreticular functionalization approach in which the desired topological net is first considered as a blueprint, and then two predesigned functionalized polydentate ligands link to four different metal clusters by de novo routes to achieve the MOFs with expected pore structure and catalytic sites. By means of this strategy, we successfully synthesized four programmed MOFs (named as URMOF-1–4) with diverse topologies, pore morphologies, and sizes and distribution of active sites. Subsequently, we systematically investigated the Friedel–Crafts reactions of 1-methylpyrrole or 1-methylindole with nitroalkene derivatives with diverse sizes to assess the catalytic properties of the above-mentioned URMOFs. These four URMOFs can act as reusable H-bond catalysts and show varied catalytic capacities and size-selectivity properties. Most significantly, the open morphologies of pores, large channels in the framework, and effective distribution of active sites on the wall of the channel are proved to facilitate catalysis. This urea-containing MOF catalytic platform provides new insight into the catalytic properties of MOFs with the same kind of active sites but diverse topologies, pore morphologies, and sizes and distributions of catalytic sites.