μ-Hydroxyl trinuclear copper(II) compounds, with core structures closely resembling the central moieties in multicopper oxidases, have been extensively investigated and the importance of the prototypes in the oxidation of C–H bonds has been confirmed. In the course of study for the Cu(II) salens catalyzing the three-component (sodium azide, epoxide and non-activated terminal alkyne) 1,3-Huisgen cycloaddition, we observed the unusual formation of a μ-OH bridging trinuclear copper cluster supported by three (R,R)-N-(5-sulfonatosalicylidene)-1,2-diaminocyclohexane ligands (Cu-6) during the catalytic process. More interestingly, through comparative studies for the activity of the mononuclear copper(II) complexes (Cu-1 and Cu-5), we found that the μ-OH trinuclear copper(II) complex (Cu-6) was the active catalyst precursor. Through analysing the reaction intermediates we found that Cu(II) was partially reduced to Cu(I) and an adduct formed during catalytic process, which involves the alkyne coordinating to the Cu centers. This is the first example where a μ-OH trinuclear copper(II) complex has been isolated in copper catalyzed reactions other than catalytic oxidations, which provides a valuable clue to investigate that μ-OH copper clusters could be the intermediates in copper catalysed reactions in aqueous media.