Abstract U-Pb and Hf-isotope analyses of zircon xenocrysts from drilling-sampled Carboniferous volcanic rocks suggest the presence of unexposed Eoarchean crust beneath the Junggar Basin (NW China), southwestern Central Asian Orogenic Belt (CAOB). The oldest zircon population with U-Pb ages of 3.8 Ga shows chondritic eHf(t) of −0.7 to +0.7, and Hf model ages of 3900–3952 Ma (TDM) and 3973–4062 Ma (Tcrust). Three slightly younger populations at 3.7, 3.62 and 3.45 Ga have eHf(t) of −5.7 to +2.4, TDM of 3.6–3.9 Ga and Tcrust of 3.7–4.1 Ga. The youngest xenocrysts yield U-Pb ages of 2.55 Ga with eHf(t) values of +3.7 to +8.0. Crustal mineral inclusions and the trace-element compositions of all these zircons show that they probably crystallized from granitic magmas. The observation of deeply hidden Archean crust significantly older than the exposed Phanerozoic upper crust suggests that the juvenile origin in CAOB may be overestimated, and the study of crustal growth rates through time for young orogens will require revision. By comparing the Hf isotopic signatures of ancient zircons (>3.4 Ga) worldwide, we infer that there may have been a great change in early crustal evolution at the Hadean–Archean transition (~3.9 Ga), possibly linked to the Late Heavy Bombardment (LHB).