Contrasting models for internal versus external locations of the South China Craton (SCC) in the supercontinent Rodinia and associated mantle plume or ocean subduction dominated tectonic processes can be resolved by detrital zircon U-Pb dating and Lu-Hf isotopic analyses on the Cryogenian Nanhua Supergroup in the central SCC. Our results show that samples from the lower Liantuo, Tiesi’ao, and Datangpo formations of the Nanhua Supergroup show three age peaks at 2.50 Ga, 2.05 Ga, and 0.85 Ga, and those of the upper Nantuo Formation yield four peaks at 2.50 Ga, 2.05 Ga, 0.85 Ga, and 0.65 Ga. The Archean and Paleoproterozoic (1.80–2.10 Ga) zircons have εHf(t) values of −16.3 to +4.7 and −23.0 to +4.2, and may be sourced from the Kongling and Douling complexes and Paleoproterozoic intrusions in the northern Yangtze Block, respectively. Early Neoproterozoic (0.70–0.96 Ga) zircon grains show variable εHf(t) values of −20.0 to +15.0. In combination with the absence of Mesoproterozoic detrital zircons in the Nanhua Supergroup, huge volumes of Neoproterozoic granitic intrusions in the northern Yangtze Block are the potential sources for the 0.70–0.96 Ga detrital zircons. Only the siltstone of the Nantuo Formation has late Neoproterozoic (0.63–0.69 Ga) detrital zircons with high and positive εHf(t) values (+7.9 to +9.4). Several granitoid intrusions (0.63–0.68 Ga) in the Wudang and Ankang uplift of the South Qinling belt in the northern Yangtze Block provide the late Neoproterozoic detrital zircons of the Nantuo Formation. These provenance analyses of the Nanhua Supergroup indicate an interior source from the SCC, rather than an exterior source from the Laurentia and Australia cratons. The Neoproterozoic rift basins and magmatic rocks in the SCC were produced by secular episodic subductions and back-arc extensions, rather than a Neoproterozoic super-mantle plume. The SCC occupied a peripheral position adjacent to northern India in Rodinia during the Neoproterozoic. These conclusions will promote our understanding of genetic mechanism and distribution prediction of the several Cryogenian–Cambrian black-shale layers and excellent source rocks in the SCC.