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The reactions of Ru3(CO)12 with alkynes R1C CR2 (R1 = pyridyl, R2 = Ph (1); R1 = pyridyl, R2 = ferrocenyl (2); R1 = R2 = Ph (3)) in toluene afforded a linear triruthenium cluster (1a/1b), a triangular triruthenium cluster (2a) and two biruthenium clusters (3a and 3b). All clusters were characterized by FT-IR, NMR, ESI-MS spectrometry and single-crystal X-ray diffraction. The structures of 1a/1b (two polymorphs) contain each a Ru3 linear skeleton, which arises from the coupling and coordination of two ligands 1 with the ruthenium centers and formation of two six-membered rings with a common edge. The structure of 2a contains a metallacyclopentadienyl framework formed by two coupled ligands 2 bonding with a triangular-arranged ruthenium skeleton via a μ4-η1:η2:η1:η1 bonding mode, and a four-membered ring formed by the third ligand 2 bonding with ruthenium atom in a μ3-η1:η1 bonding mode and linking of its pyridyl N atom with another ruthenium atom. The reaction of 3 and Ru3(CO)12 in toluene gave unexpected ruthenole 3a and a reported cluster 3b. A detailed investigation on the reaction processes suggested that the nitrogen atoms of the pyridyl groups in the alkyne ligand 1–2 directs the formation of the triruthenium clusters 1a/1b and 2a. The electronic and steric effects of a ferrocenyl group are distinctly different from those of a phenyl group and lead to the diverse structures of the products 1a/1b and 2a in the reactions of Ru3(CO)12 with alkynes 1–2, respectively. Moreover, the solvent properties exert great effects on the product distribution.