Finite cluster models are widely used to study the photophysics and photochemistry of metal−organic frameworks, yet their construction is often arbitrary and lacks systematic benchmarking. Boundary truncation and capping can contaminate frontier orbitals and even introduce artificial near-frontier orbitals, leading to substantial misinterpretation of excited-state character and photobehavior. Here, we systematically benchmark four representative MIL-125 cluster models containing different numbers of inorganic nodes and organic linkers across eight density functionals. We compare their local structure, fundamental and optical gaps, electron−hole centroid distance in the first ligand-to-metal charge-transfer state, atomic charges, frontier orbitals, and low-energy excitation landscapes. It was found that the hybrid functionals with a low fraction of Hartree−Fock exchange are providing a more reasonable description of both ground and excited states, with HSE06 giving the most balanced overall performance. Among the models examined, the cluster containing two inorganic nodes connected by one organic linker shows the closest overall agreement with the periodic reference while avoiding contaminated frontier orbitals and artificial orbitals. By contrast, the fully capped single-node model and the most compact single-node single-linker model exhibit pronounced truncation- and capping-induced contamination of frontier orbitals and artificial orbitals, whereas the single-node four-linker model remains useful for interligand analysis despite residual artifacts. These results provide physically grounded guidelines for cluster-model construction and density-functional selection in MIL-125.