Magmatic systems exposed at the surface can sample the deep crust during the ascent of magmas from deep lithosphere. Zircons captured by such rocks, especially those with pre-eruption ages (xenocrysts), can be used to extract information on the formation and evolution of the deep continental crust. Integrated U–Pb dating and Hf-isotope analysis of zircon xenocrysts from the Cenozoic (<30 Ma) basalts on the Leizhou Peninsula, in the southwestern part of the Cathaysia Block of South China, offer a unique glimpse at the evolution of the deep crust beneath the block. 90 zircons from the basalts yield concordant or nearly concordant U–Pb ages varying from 2726 Ma to 61 Ma. There are a few Archean ages (2.7–2.5 Ga), but the majority of zircons fall into Proterozoic, Early Paleozoic (most strongly represented) and Mesozoic age populations. The oldest grain (2.7 Ga) has εHf(t) of −9.5, corresponding to a TDM model age of 3.4 Ga and a Tcrust model age of 3.8 Ga, respectively, while 30% of the analyzed grains have Tcrust model ages ≥2.5 Ga. The zircons in the basalts also record multiple post-Archean tectono-thermal events, including 1.9–1.7 Ga, 1.4–1.2 Ga, 1.0–0.8 Ga, 600–450 Ma, 250–150 Ma. These thermal events, and particularly the strong Caledonian and obvious Indosinian events are similar to those recorded in the Yunkai, Naling and Wuyi regions. The similarity between the studied area and these other regions indicates that the Leizhou Peninsula, covered by Quaternary volcanic rocks and sedimentary rocks, represents the southwestern part of the Cathaysia Block. The zircons with ages of Paleoproterozoic (1.9–1.7 Ga), late Mesoproterozoic (1.0–0.8 Ga) events have positive εHf(t), up to +10.2, showing the addition of juvenile mantle-derived materials in these three periods. Meanwhile, those with ages of the early Mesoproterozoic (1.4–1.2 Ga), late Neoproterozoic to early Paleozoic (650–550 Ma), Phanerozoic (400–450 Ma, 250–150 Ma) have negative εHf(t), down to −35, suggesting the reworking of old crustal components at these times. These data imply that there are significant volumes of Paleoarchean to Mesoarchean (>3.4 Ga) components (or remnants) as old as 3.8 Ga beneath the studied area. Combining with the scattered Archean ages in other parts of the Cathaysia Block (such as Guangxi, Yunkai, Naling and Wuyi), they suggest that ancient deep crustal components may be more widely distributed than would be indicated by the exposed rocks in the block.