Granitoid magmatism is extensively developed in the Altai Superterrane, but the timing of magmatic events is not so well determined. In this study, twelve granitoid intrusions from Southwest Mongolia were dated by the zircon U–Pb method and analyzed for zircon Hf isotopic compositions. The new age data indicated three phases of magmatic emplacement: Middle Paleozoic (398–350Ma), Late Paleozoic (317–289Ma) and Triassic (ca. 244–211Ma). The first-phase magmatism is mainly composed of hornblende-bearing I-type granitoids, formed during a long-lasting subduction process in the Early to Middle Paleozoic. The second-phase magmatism was manifested by a few small intrusions, primarily distributed along the Erqis fault zone, and probably formed in a transitional tectonic regime from subduction to post-tectonic setting in the Late Paleozoic. The third-phase magmatism was represented by post-tectonic granitoids emplaced in an intraplate extensional setting. Model ages that were calculated using the composition of new continental crust are predominantly Neoproterozoic to Early Paleozoic, indicating that the protoliths of granitoids were likely dominated by Paleozoic juvenile crust with minor Neoproterozoic materials. The Altai Superterrane was a huge Paleozoic tectonic collage produced by amalgamation of subduction–accretion complexes in the margin of the Siberian continent and the Tuva–Mongol microcontinent.