The in situ zircon U-Pb-Lu-Hf isotope records from end-Permian volcanic interlayers in southwest China, integrated with previous studies, restructure the evolutionary history of the Yangtze Craton from Precambrian to Late Paleozoic. This includes early continental crust formation before ~3.0 Ga and massive juvenile crustal growth at 2.6–2.4 Ga; large-scale crustal reworking at ~2.1–1.7 Ga; Neoproterozoic crust addition at ~1.1 to 0.7 Ga; collision and subduction along the craton margin between ~700–541 Ma; Early Ordovician to Late Silurian magmatism; and large tectono-thermal events in the Middle Carboniferous to end-Permian. Some zircons with TMD2 ages from 4.40 to 4.01 Ga and lower initial 176Hf/177Hf values of 0.280592 to 0.280726 may imply the existence of Hadean crust relics beneath the Yangtze Craton and their provenances could be associated with Hadean crustal remelting. This study further clarifies that the Precambrian-age zircons between the end-Permian volcanic interlayers, the complexes in the western margin of the Yangtze Craton, and the sedimentary Kangdian Basin, may share an affinity based on similar U-Pb age spectra and Hf isotope features. It also shows that the Neoproterozoic tectono-thermal event may be associated with large-scale tectono-rifting activity, which is different from the Grenville-age continental collision between Yangtze and Cathaysia blocks in South China. The above findings support the inference of a widespread Archean basement extending to the western Yangtze Craton and a provenance in the Kangdian Basin that is derived from the weathering and erosion of Paleoproterozoic continental crust.