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Understanding the thermal aggregation behavior of metal atoms is important for the synthesis of supported metal clusters. Here, derived from a metal–organic framework encapsulating a trinuclear Fe^III₂Fe^II complex (denoted as Fe₃) within the channels, a well‐defined nitrogen‐doped carbon layer is fabricated as an ideal support for stabilizing the generated iron nanoclusters. Atomic replacement of Fe^II by other metal(II) ions (e.g., Zn^II/Co^II) via synthesizing isostructural trinuclear‐complex precursors (Fe₂Zn/Fe₂Co), namely the “heteroatom modulator approach”, is inhibiting the aggregation of Fe atoms toward nanoclusters with formation of a stable iron dimer in an optimal metal–nitrogen moiety, clearly identified by direct transmission electron microscopy and X‐ray absorption fine structure analysis. The supported iron dimer, serving as cooperative metal–metal site, acts as efficient oxygen evolution catalyst. Our …