The basement beneath the Caledonian belt in SE China has been overprinted by Indosinian and Yanshanian events and is poorly known. In situ U-Pb and Hf-isotope analysis of zircons from granites and surrounding rocks in the Nanling Mountains area of the fold belt reveal that the Lanhe felsic gneiss is an outcrop of Mesoproterozoic basement, probably with a partly Late Archean protolith. This is consistent with Nd model ages of granites in this region, and exposures of Cathaysia basement in the coastal area of SE China. In the Nanling Mountains, this basement was reactivated to generate granitoid rocks during the Caledonian, Indosinian, and Yanshanian tectonothermal events. The Caledonian overprint is documented in extensive exposures of the Zhuguang migmatites (425–470 Ma) and by previous U-Pb zircon dating of adjacent granites. The Jiangnan granite may be of similar age, but strongly reworked. The Indosinian overprint resulted in the formation of granites such as the Luxi and Xiazhuang bodies (233–246 Ma) in the Guidong complex. The Yanshanian overprint produced the most widely distributed granites (circa 160 Ma) such as the Jiufeng and Fogang bodies, and parts of the Guidong complex. Hf-isotope data show that all of the Phanerozoic magmatic rocks were derived from the Mesoproterozoic basement (and minor Archean components), without obvious contributions from juvenile sources. The presence of zircons with Archean age (2.5–2.7 Ga) in both the Lanhe gneiss and Devonian sediments indicates that the Badu and Mayuan groups may not be the oldest basement of the Cathaysia block. Some Archean basement (circa 2.5–2.7 Ga) may still be exposed but unrecognized in this region, and Cathaysia may include Archean microcontinental fragments.