The Khoy metamorphic complex (KMC) consists of metabasite, metagranite and some metasediments,which are overlain by the Oligo-Miocene Qom formation. Because there are no reliable stratigraphic sequences or isotope dating data available, discordant ages for the formation and tectonic setting of the KMC have been proposed by many studies. For example, various studies have suggested a Jurassic age, Cretaceous age or younger age. In the present study, new isotopic information based on U–Pb zircon and Rb–Sr mineral isochron dating has revealed the origin and timing of metamorphism for the KMC. These new results do not confirm the previously proposed ages. The results of U–Pb dating from 65 points in the core and rings of zircon minerals from the metagranite and metabasite rocks suggests a late Proterozoic (550–590 Ma) consolidation of granitic and basaltic magma. In addition, Rb–Sr mineral isochron dating indicates that the metamorphism occurred 146Ma ago. Finally, mylonitic foliation overprinted the metamorphicand granitic complex, probably occurring in the pre-Oligocene. Furthermore, initial 143Nd/144Nd and 87Sr/86Sr ratios strongly suggest that the original basic magma formed in a depleted mantle in the subduction zone, with some contamination from recycled sediments.