Heterogeneous catalysis plays an indispensable role in chemical production and energy conversion. Incorporation of transition metals into metal oxides and zeolites is a common strategy to fine-tune the activity and selectivity of the resulting solid catalysts, as either the active center or promotor. Studying the underlying mechanism is however challenging. Decorating the metal-oxo clusters with transition metals in metal-organic frameworks (MOFs) via postsynthetic modification offers a rational approach to construct well-defined structural models for better understanding of the reaction mechanism. Therefore, it is important to expand the materials scope beyond the currently widely studied zirconium MOFs consisting of Zr6 nodes. In this work, we report the design and synthesis of a new (4,12)-connected Zr-MOF with ith topology that consists of rare Zr9 nodes. FeIII was further incorporated onto the Zr9 nodes of the framework, and the resulting MOF material exhibits significantly enhanced activity and selectivity toward the photocatalytic oxidation of toluene. This work demonstrates a delicate ligand design strategy to control the nuclearity of Zr-oxo clusters, which further dictates the number and binding sites of transition metals and the overall photocatalytic activity toward C-H activation. Our work paves the way for future exploration of the structure-activity study of catalysts using MOFs as the model system.