The [Zn4O]6+ cluster is well-known to form the archetypal MOF-5 topology with dicarboxylate ligands. Here we report two new materials (CPM-300 and -301) that show dramatic alteration of topological and chemical behaviors of [Zn4O]6+ clusters. In CPM-300, [Zn4O]6+ untypically forms the MIL-88/MOF-235 type framework with a small pentane-ring-based chiral dicarboxylate. In contrast, in CPM-301, when mediated by [Zn9(btz)12]6+ clusters (btz = benzotriazolate), the MOF-5 topology is regenerated with the same chiral ligand, albeit with alternating [Zn4O]6+ and [Zn9(btz)12]6+ clusters. Importantly, both CPM-300 and CPM-301 are homochiral, hydrothermally stable in boiling water and alcohol, and thermally stable to 440 °C or higher. It is concluded that small methyl groups on the chiral ligand is sufficiently powerful to shield [Zn4O]6+ clusters from degradation by water, even at high temperatures. These results reveal a promising platform for the development of a new class of cluster-based homochiral and hydrothermally stable porous materials.