Zircon U–Pb and Hf isotope data integrated in this study for magmatic and metamorphic rocks from the Hida Belt, southwest Japan, lead to a new understanding of the evolution of the Cordilleran arc system along the ancestral margins of present-day Northeast Asia. Ion microprobe data for magmatic zircon domains from eight mafic to intermediate orthogneisses in the Tateyama and Tsunogawa areas yielded weighted mean 206Pb/238U ages spanning the entire Permian period (302–254 Ma). Under cathodoluminescence, primary magmatic growth zones in the zircon crystals were observed to be partially or completely replaced by inward-penetrating, irregularly curved featureless or weakly zoned secondary domains that mostly yielded U–Pb ages of 250–240 Ma and relatively high Th/U ratios (> 0.2). These secondary domains are considered to have been formed by solid-state recrystallization during thermal overprints associated with intrusions of Hida granitoids. Available whole-rock geochemical and Sr–Nd isotope data as well as zircon age spectra corroborate that the Hida Belt comprises the Paleozoic–Mesozoic Cordilleran arc system built upon the margin of the North China Craton, together with the Yeongnam Massif in southern Korea. The arc magmatism along this system was commenced in the Carboniferous and culminated in the Permian–Triassic transition period. Highly positive εHf(t) values (> +12) of late Carboniferous to early Permian detrital zircons in the Hida paragneisses indicate that there was significant input from the depleted asthenospheric mantle and/or its crustal derivatives in the early stage of arc magmatism. On the other hand, near-chondritic εHf(t) values (+5 to −2) of magmatic zircons from late Permian Hida orthogneisses suggest a lithospheric mantle origin. Hf isotopic differences between magmatic zircon cores and the secondary rims observed in some orthogneiss samples clearly indicate that the zircons were chemically open to fluids or melts during thermal overprints. Resumed highly positive zircon εHf(t) values (>+9) shared by Early Jurassic granitoids in the Hida Belt and Yeongnam Massif may reflect reworking of the Paleozoic arc crust.