U-Pb dating (SHRIMP-II) and study of the internal structure and composition were carried out for zircon from hypersthene gneiss from the Irkut granulite-gneiss block (Sharyzhalgai uplift in the southwestern Siberian craton). Three generations of zircon have been revealed in the hypersthene gneiss, which differ in zoning pattern, U and Th concentrations, and REE distribution. Zircon cores with growth zoning relics show a REE pattern typical of magmatic zircon: with a high (Lu/Gd)n value (11–36) and a distinct Ce anomaly (Ce/Ce* = 15–81). They belong to early magmatic generation with an age of ≥3.16 Ga. Multifaced soccerball crystals, rims, and unzoned cores of zircon belong to metamorphic generation; they are depleted in REE and show a lower (Lu/Gd)n value (1.1–9.2) than the magmatic cores. This zircon generation formed as a result of the Mesoarchean high-temperature metamorphism at ~3.04 Ga. The latest zircon generation includes thin outer rims with low (Lu/Gd)n (11–12.4) and Th/U (0.02–0.05) values and long-prismatic crystals with an oscillatory zoning, which resulted from the Paleoproterozoic (~1.85 Ga) granulite metamorphism and partial melting. The different ages of high-temperature metamorphism in the granulite-gneiss (~3.04 and 2.55–2.6 Ga) and granite-greenstone (~3.2 Ga) blocks of the Sharyzhalgai uplift reflect the independent tectonothermal and geodynamic evolution of crust in these structures, up to the final amalgamation in the Paleoproterozoic (1.88–1.85 Ga).