Detailed LAM-ICPMS U–Pb dating and LAM-MC-ICPMS Lu–Hf isotope analysis were carried out on zircons from nine samples of basement metamorphic rocks in the southern Cathaysia Block, South China. The chemical compositions of these metamorphic rocks and zircon morphology indicate that their protoliths were sedimentary; zircon U–Pb dating results show they mainly formed during the late Neoproterozoic. The Precambrian crust of the Cathaysia Block can be divided into two distinct tectonic domains, the Wuyishan terrane to the northeast and the Nanling-Yunkai terrane to the southwest. The nearly E–W boundary between these two terranes is also supported by geophysical, petrological and geochemical evidence, and the basement rocks of the two terranes are comprised of different components. The Wuyishan terrane is characterized by dominant Paleoproterozoic (1.86 Ga) and lesser Neoarchean magmatism, and the southern-central part of the terrane suffered strong Neoproterozoic and early Paleozoic tectonothermal reworking. The zircon data suggest that there were five important episodes of juvenile crust generation (3.6 Ga, 2.8 Ga, 2.6–2.4 Ga, 1.85 Ga and 0.8–0.7 Ga) in the Wuyishan terrane. Strong Paleoproterozoic (1.85 Ga) magmatism in northern Wuyishan and Neoproterozoic (0.8–0.7 Ga) magmatism in central and southern Wuyishan both principally involved the remelting of old crust with minor input of juvenile material. In contrast, the Nanling-Yunkai terrane contains abundant Neoarchean and Grenvillian zircons, some evidence of Mesoproterozoic activity and rare Paleo- to Meso-Archean and Neoproterozoic zircons. U–Pb ages and Hf-isotopic compositions of the detrital zircons from the late Neoproterozoic to early Paleozoic meta-sedimentary rocks in the Nanling-Yunkai area suggest that the growth of juvenile crust mainly occurred at ~3.6 Ga, ~3.3 Ga, 2.5–2.6 Ga, ~1.6 Ga, ~1.0 Ga and 0.8–0.7 Ga. Neoarchaean (2.6–2.5 Ga), Grenvillian (~1.0 Ga) and Neoproterozoic (0.8–0.7 Ga) magmatism mainly involved the recycling of old crust. Minor remnants of ~4.1 Ga crust may remain in the terrane. This crustal history is distinct from that of the Wuyishan terrane and analogous to those recorded for the eastern India–East Antarctic domain of northern Gondwanaland, suggesting that they probably were once linked.